| Next changeset 1:b433586432d7 (2015-03-24) |
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._ITSx ._ITSx.xml ._ITSx_db ._tool_dependencies.xml ITSx ITSx.xml ITSx_db/.DS_Store ITSx_db/._.DS_Store ITSx_db/._HMMs ITSx_db/HMMs/._A.hmm ITSx_db/HMMs/._A.hmm.h3f ITSx_db/HMMs/._A.hmm.h3i ITSx_db/HMMs/._A.hmm.h3m ITSx_db/HMMs/._A.hmm.h3p ITSx_db/HMMs/._B.hmm ITSx_db/HMMs/._B.hmm.h3f ITSx_db/HMMs/._B.hmm.h3i ITSx_db/HMMs/._B.hmm.h3m ITSx_db/HMMs/._B.hmm.h3p ITSx_db/HMMs/._C.hmm ITSx_db/HMMs/._C.hmm.h3f ITSx_db/HMMs/._C.hmm.h3i ITSx_db/HMMs/._C.hmm.h3m ITSx_db/HMMs/._C.hmm.h3p ITSx_db/HMMs/._D.hmm ITSx_db/HMMs/._D.hmm.h3f ITSx_db/HMMs/._D.hmm.h3i ITSx_db/HMMs/._D.hmm.h3m ITSx_db/HMMs/._D.hmm.h3p ITSx_db/HMMs/._E.hmm ITSx_db/HMMs/._E.hmm.h3f ITSx_db/HMMs/._E.hmm.h3i ITSx_db/HMMs/._E.hmm.h3m ITSx_db/HMMs/._E.hmm.h3p ITSx_db/HMMs/._F.hmm ITSx_db/HMMs/._F.hmm.h3f ITSx_db/HMMs/._F.hmm.h3i ITSx_db/HMMs/._F.hmm.h3m ITSx_db/HMMs/._F.hmm.h3p ITSx_db/HMMs/._G.hmm ITSx_db/HMMs/._G.hmm.h3f ITSx_db/HMMs/._G.hmm.h3i ITSx_db/HMMs/._G.hmm.h3m ITSx_db/HMMs/._G.hmm.h3p ITSx_db/HMMs/._H.hmm ITSx_db/HMMs/._H.hmm.h3f ITSx_db/HMMs/._H.hmm.h3i ITSx_db/HMMs/._H.hmm.h3m ITSx_db/HMMs/._H.hmm.h3p ITSx_db/HMMs/._I.hmm ITSx_db/HMMs/._I.hmm.h3f ITSx_db/HMMs/._I.hmm.h3i ITSx_db/HMMs/._I.hmm.h3m ITSx_db/HMMs/._I.hmm.h3p ITSx_db/HMMs/._L.hmm ITSx_db/HMMs/._L.hmm.h3f ITSx_db/HMMs/._L.hmm.h3i ITSx_db/HMMs/._L.hmm.h3m ITSx_db/HMMs/._L.hmm.h3p ITSx_db/HMMs/._M.hmm ITSx_db/HMMs/._M.hmm.h3f ITSx_db/HMMs/._M.hmm.h3i ITSx_db/HMMs/._M.hmm.h3m ITSx_db/HMMs/._M.hmm.h3p ITSx_db/HMMs/._N.hmm ITSx_db/HMMs/._O.hmm ITSx_db/HMMs/._O.hmm.h3f ITSx_db/HMMs/._O.hmm.h3i ITSx_db/HMMs/._O.hmm.h3m ITSx_db/HMMs/._O.hmm.h3p ITSx_db/HMMs/._P.hmm ITSx_db/HMMs/._P.hmm.h3f ITSx_db/HMMs/._P.hmm.h3i ITSx_db/HMMs/._P.hmm.h3m ITSx_db/HMMs/._P.hmm.h3p ITSx_db/HMMs/._Q.hmm ITSx_db/HMMs/._Q.hmm.h3f ITSx_db/HMMs/._Q.hmm.h3i ITSx_db/HMMs/._Q.hmm.h3m ITSx_db/HMMs/._Q.hmm.h3p ITSx_db/HMMs/._R.hmm ITSx_db/HMMs/._R.hmm.h3f ITSx_db/HMMs/._R.hmm.h3i ITSx_db/HMMs/._R.hmm.h3m ITSx_db/HMMs/._R.hmm.h3p ITSx_db/HMMs/._S.hmm ITSx_db/HMMs/._S.hmm.h3f ITSx_db/HMMs/._S.hmm.h3i ITSx_db/HMMs/._S.hmm.h3m ITSx_db/HMMs/._S.hmm.h3p ITSx_db/HMMs/._T.hmm ITSx_db/HMMs/._T.hmm.h3f ITSx_db/HMMs/._T.hmm.h3i ITSx_db/HMMs/._T.hmm.h3m ITSx_db/HMMs/._T.hmm.h3p ITSx_db/HMMs/._U.hmm ITSx_db/HMMs/._U.hmm.h3f ITSx_db/HMMs/._U.hmm.h3i ITSx_db/HMMs/._U.hmm.h3m ITSx_db/HMMs/._U.hmm.h3p ITSx_db/HMMs/A.hmm ITSx_db/HMMs/A.hmm.h3f ITSx_db/HMMs/A.hmm.h3i ITSx_db/HMMs/A.hmm.h3m ITSx_db/HMMs/A.hmm.h3p ITSx_db/HMMs/B.hmm ITSx_db/HMMs/B.hmm.h3f ITSx_db/HMMs/B.hmm.h3i ITSx_db/HMMs/B.hmm.h3m ITSx_db/HMMs/B.hmm.h3p ITSx_db/HMMs/C.hmm ITSx_db/HMMs/C.hmm.h3f ITSx_db/HMMs/C.hmm.h3i ITSx_db/HMMs/C.hmm.h3m ITSx_db/HMMs/C.hmm.h3p ITSx_db/HMMs/D.hmm ITSx_db/HMMs/D.hmm.h3f ITSx_db/HMMs/D.hmm.h3i ITSx_db/HMMs/D.hmm.h3m ITSx_db/HMMs/D.hmm.h3p ITSx_db/HMMs/E.hmm ITSx_db/HMMs/E.hmm.h3f ITSx_db/HMMs/E.hmm.h3i ITSx_db/HMMs/E.hmm.h3m ITSx_db/HMMs/E.hmm.h3p ITSx_db/HMMs/F.hmm ITSx_db/HMMs/F.hmm.h3f ITSx_db/HMMs/F.hmm.h3i ITSx_db/HMMs/F.hmm.h3m ITSx_db/HMMs/F.hmm.h3p ITSx_db/HMMs/G.hmm ITSx_db/HMMs/G.hmm.h3f ITSx_db/HMMs/G.hmm.h3i ITSx_db/HMMs/G.hmm.h3m ITSx_db/HMMs/G.hmm.h3p ITSx_db/HMMs/H.hmm ITSx_db/HMMs/H.hmm.h3f ITSx_db/HMMs/H.hmm.h3i ITSx_db/HMMs/H.hmm.h3m ITSx_db/HMMs/H.hmm.h3p ITSx_db/HMMs/I.hmm ITSx_db/HMMs/I.hmm.h3f ITSx_db/HMMs/I.hmm.h3i ITSx_db/HMMs/I.hmm.h3m ITSx_db/HMMs/I.hmm.h3p ITSx_db/HMMs/L.hmm ITSx_db/HMMs/L.hmm.h3f ITSx_db/HMMs/L.hmm.h3i ITSx_db/HMMs/L.hmm.h3m ITSx_db/HMMs/L.hmm.h3p ITSx_db/HMMs/M.hmm ITSx_db/HMMs/M.hmm.h3f ITSx_db/HMMs/M.hmm.h3i ITSx_db/HMMs/M.hmm.h3m ITSx_db/HMMs/M.hmm.h3p ITSx_db/HMMs/N.hmm ITSx_db/HMMs/O.hmm ITSx_db/HMMs/O.hmm.h3f ITSx_db/HMMs/O.hmm.h3i ITSx_db/HMMs/O.hmm.h3m ITSx_db/HMMs/O.hmm.h3p ITSx_db/HMMs/P.hmm ITSx_db/HMMs/P.hmm.h3f ITSx_db/HMMs/P.hmm.h3i ITSx_db/HMMs/P.hmm.h3m ITSx_db/HMMs/P.hmm.h3p ITSx_db/HMMs/Q.hmm ITSx_db/HMMs/Q.hmm.h3f ITSx_db/HMMs/Q.hmm.h3i ITSx_db/HMMs/Q.hmm.h3m ITSx_db/HMMs/Q.hmm.h3p ITSx_db/HMMs/R.hmm ITSx_db/HMMs/R.hmm.h3f ITSx_db/HMMs/R.hmm.h3i ITSx_db/HMMs/R.hmm.h3m ITSx_db/HMMs/R.hmm.h3p ITSx_db/HMMs/S.hmm ITSx_db/HMMs/S.hmm.h3f ITSx_db/HMMs/S.hmm.h3i ITSx_db/HMMs/S.hmm.h3m ITSx_db/HMMs/S.hmm.h3p ITSx_db/HMMs/T.hmm ITSx_db/HMMs/T.hmm.h3f ITSx_db/HMMs/T.hmm.h3i ITSx_db/HMMs/T.hmm.h3m ITSx_db/HMMs/T.hmm.h3p ITSx_db/HMMs/U.hmm ITSx_db/HMMs/U.hmm.h3f ITSx_db/HMMs/U.hmm.h3i ITSx_db/HMMs/U.hmm.h3m ITSx_db/HMMs/U.hmm.h3p tool_dependencies.xml |
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| diff -r 000000000000 -r f82c70f54bd7 ITSx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx Tue Mar 24 12:02:48 2015 -0400 |
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| b'@@ -0,0 +1,2695 @@\n+#!/usr/bin/perl\n+# ITSx ITS Extractor\n+$app_title = "ITSx -- Identifies ITS sequences and extracts the ITS region";\n+$app_author = "Johan Bengtsson-Palme et al., University of Gothenburg";\n+$app_version = "1.0.11";\n+$app_message = "";\n+# ----------------------------------------------------------------- #\n+\n+# License information\n+$license =\n+" ITSx - ITS Extractor -- Identifies ITS sequences and extracts the ITS region\\\n+ Copyright (C) 2012-2014 Johan Bengtsson-Palme et al.\\\n+\\\n+ This program is free software: you can redistribute it and/or modify\\\n+ it under the terms of the GNU General Public License as published by\\\n+ the Free Software Foundation, either version 3 of the License, or\\\n+ (at your option) any later version.\\\n+\\\n+ This program is distributed in the hope that it will be useful,\\\n+ but WITHOUT ANY WARRANTY; without even the implied warranty of\\\n+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\\\n+ GNU General Public License for more details.\\\n+\\\n+ You should have received a copy of the GNU General Public License\\\n+ along with this program, in a file called \'license.txt\'\\\n+ If not, see: http://www.gnu.org/licenses/.\\\n+";\n+\n+## BUGS:\n+$bugs = "New features in this version ($app_version):\\\n+- None\\\n+\\\n+Fixed bugs in this version ($app_version):\\\n+- Fixed a bug causing newline characters to be occasionally skipped in the \'its1.full_and_partial.fasta\' FASTA output file when the \'--anchor\' option was used\\\n+\\\n+Known bugs in this version ($app_version):\\\n+- None\\\n+";\n+\n+## OPTIONS:\n+$options = "\\\n+-i {file} : DNA FASTA input file to investigate\\\n+-o {file} : Base for the names of output file(s)\\\n+-p {directory} : A path to a directory of HMM-profile collections representing ITS conserved regions, default is in the same directory as ITSx itself\\\n+--date {T or F} : Adds a date and time stamp to the output directory, off (F) by default\\\n+--reset {T or F} : Re-creates the HMM-database before ITSx is run, off (F) by default\\\n+\n+Sequence selection options:\\\n+-t {character code} : Profile set to use for the search, see the User\'s Guide (comma-separated), default is all\\\n+-E {value} : Domain E-value cutoff for a sequence to be included in the output, default = 1e-5\\\n+-S {value} : Domain score cutoff for a sequence to be included in the output, default = 0\\\n+-N {value} : The minimal number of domains that must match a sequence before it is included, default = 2\\\n+--selection_priority {sum, domains, eval, score} : Selects what will be of highest priority when determining the origin of the sequence, default is sum\\\n+--search_eval {value} : The E-value cutoff used in the HMMER search, high numbers may slow down the process, cannot be used with the --search_score option, default is 0.01\\\n+--search_score {value} : The score cutoff used in the HMMER search, low numbers may slow down the process, cannot be used with the --search_eval option, default is to used E-value cutoff, not score\\\n+--allow_single_domain {e-value,score or F} : Allow inclusion of sequences that only find a single domain, given that they meet the given E-value and score thresholds, on with parameters 1e-9,0 by default\\\n+--allow_reorder {T or F} : Allows profiles to be in the wrong order on extracted sequences, off (F) by default\\\n+--complement {T or F} : Checks both DNA strands against the database, creating reverse complements, on (T) by default\\\n+--cpu {value} : the number of CPU threads to use, default is 1\\\n+--multi_thread {T or F} : Multi-thread the HMMER-search, on (T) if number of CPUs (--cpu option > 1), else off (F) by default\\\n+--heuristics {T or F} : Selects whether to use HMMER\'s heuristic filtering, off (F) by default\\\n+\n+Output options:\\\n+--summary {T or F} : Summary of results output, on (T) by default\\\n+--graphical {T or F} : \'Graphical\' output, on (T) by default\\\n+--fasta {T or F} : FASTA-format output of extracted ITS sequences, on (T) by default\\\n+--preserve {T or '..b'ng time for the analysis\n+ close (SUMMARY); # Close summary file\n+ }\n+}\n+\n+sub hmmerSearch {\n+ $hmmerCommand = $_[0];\n+ $outputFile = $_[1];\n+ $strand = $_[2];\n+ $profileSet = $_[3];\n+ open (HMMEROUTPUT, ">$outputFile");\n+ open (HMMER, "$hmmerCommand |");\n+ $totalHitCount = 0;\n+ $hitCount = 0;\n+ $SSUCount = 0;\n+ $LSUCount = 0;\n+ $startCount = 0;\n+ $endCount = 0;\n+ $maxCount = 1;\n+ while (chomp($line = <HMMER>)) {\n+ if (substr($line,0,6) eq "Query:") {\n+ $hitCount = 0;\n+ $SSUCount = 0;\n+ $LSUCount = 0;\n+ $startCount = 0;\n+ $endCount = 0;\n+ undef @bestScore;\n+ undef @bestEntry;\n+ \n+ $query = substr($line,7);\n+ $queryLength = $query;\n+ $queryLength =~ s/.* *//;\n+ $queryLength =~ s/[^0-9]//g;\n+ $query =~ s/ *//;\n+ $query =~ s/ *.*//;\n+ \n+ print HMMEROUTPUT "## New query:\\t$query\\t$queryLength\\n";\n+\n+ }\n+ if (substr($line,0,12) eq "Description:") {\n+ $desc = $line;\n+ }\n+ if (substr($line,0,3) eq ">> ") {\n+ ($tempshit,$hmmerSubjectName) = split(\' \',$line);\n+ }\n+ if ($line =~ m/[0-9] ! /) {\n+ $stats = $line;\n+ $stats =~ s/ */\\t/g;\n+ ($empty,$no,$excl,$score) = split(\'\\t\',$stats);\n+ $hitCount++;\n+ $totalHitCount++;\n+ if ($maxCount == 0) {\n+\tprint HMMEROUTPUT "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+ } else {\n+\tif (substr($hmmerSubjectName,0,5) eq "1_SSU") {\n+\t $SSUCount++;\n+\t if ($SSUCount <= $maxCount) {\n+\t @bestScore[1] = $score;\n+\t @bestEntry[1] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+\t } else {\n+\t if ($score > @bestScore[1]) {\n+\t @bestScore[1] = $score;\n+\t @bestEntry[1] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+\t }\n+\t }\n+\t}\n+\tif (substr($hmmerSubjectName,0,5) eq "4_LSU") {\n+\t $LSUCount++;\n+\t if ($LSUCount <= $maxCount) {\n+\t @bestScore[4] = $score;\n+\t @bestEntry[4] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+\t } else { \n+\t if ($score > @bestScore[4]) {\n+\t @bestScore[4] = $score;\n+\t @bestEntry[4] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+\t }\n+\t }\n+\t}\n+\tif (substr($hmmerSubjectName,0,5) eq "2_5.8") {\n+\t $startCount++;\n+\t if ($startCount <= $maxCount) {\n+\t @bestScore[2] = $score;\n+\t @bestEntry[2] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+\t } else {\n+\t if ($score > @bestScore[2]) {\n+\t @bestScore[2] = $score;\n+\t @bestEntry[2] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+\t }\n+\t }\n+\t}\n+\tif (substr($hmmerSubjectName,0,5) eq "3_End") {\n+\t $endCount++;\n+\t if ($endCount <= $maxCount) {\n+\t @bestScore[3] = $score;\n+\t @bestEntry[3] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n";\n+\t } else {\n+\t if ($score > @bestScore[3]) {\n+\t @bestScore[3] = $score;\n+\t @bestEntry[3] = "$query\\t$hmmerSubjectName\\t$queryLength$stats\\n"\n+\t }\n+\t }\n+\t}\n+ }\n+ }\n+ if (substr($line,0,2) eq "//") {\n+ if ($maxCount > 0) {\n+\tif ($SSUCount > 0) {\n+\t print HMMEROUTPUT @bestEntry[1];\n+\t}\n+\tif ($startCount > 0) {\n+\t print HMMEROUTPUT @bestEntry[2];\n+\t}\n+\tif ($endCount > 0) {\n+\t print HMMEROUTPUT @bestEntry[3];\n+\t}\n+\tif ($LSUCount > 0) {\n+\t print HMMEROUTPUT @bestEntry[4];\n+\t}\n+ }\n+ print HMMEROUTPUT "//\\n";\n+ }\n+ }\n+ close(HMMEROUTPUT);\n+ $now = localtime;\n+ if ($silent == 0) {\n+ if ($strand eq "M") {\n+ print STDERR " $now : " . ucfirst($profileIndex{$profileSet}) . " analysis of main strand finished.\\n"; # Print finished type\n+ } else {\n+ print STDERR " $now : " . ucfirst($profileIndex{$profileSet}) . " analysis of complementary strand finished.\\n"; # Print finished type\n+ }\n+ }\n+}\n+\n+\n+## Please send beers, pizzas, cakes, fruit pies, job positions and other types of feedback to:\n+## johan.bengtsson [at] microbiology.se\n+## Looking forward to hearing from you.... visit my website: www.microbiology.se for info on my research\n+## //Johan Bengtsson, 2012-2014\n' |
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| diff -r 000000000000 -r f82c70f54bd7 ITSx.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx.xml Tue Mar 24 12:02:48 2015 -0400 |
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| b'@@ -0,0 +1,172 @@\n+<tool id="ITSx" name="ITSx Extractor" version="1.0.6">\n+\n+ <description> \n+ ITSx -- Identifies ITS sequences and extracts the ITS region\n+ </description>\n+\n+ <command interpreter="perl">\n+ ITSx -i $input --detailed_results T --cpu $cpu $preserve $reset \n+ </command>\n+ <requirements>\n+\t<requirement type="package" version="3.1b1">hmmer</requirement>\n+ </requirements>\n+ <inputs>\n+\t<param name="input" type="data" format="fasta" label="Input Fasta"/>\n+\t<param name="cpu" type="integer" value="1" label="cpu"/>\n+\t<param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Checks both DNA strands against the database"/>\n+\t<param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER\'s heuristic filtering"/>\n+\t<param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/>\n+\t<param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/>\n+ </inputs>\n+\n+ <outputs>\n+ <data name="ITS1" format="fasta" label="Extracted ITS1 Fasta File" from_work_dir="ITSx_out.ITS1.fasta"/>\n+ <data name="ITS2" format="fasta" label="Extracted ITS2 Fasta File" from_work_dir="ITSx_out.ITS2.fasta"/>\n+ <data name="fullfasta" format="fasta" label="Full Fasta of ITS extracted" from_work_dir="ITSx_out.full.fasta"/>\n+ <data name="graph" format="txt" label="Graph of ITS regions" from_work_dir="ITSx_out.graph"/>\n+ <data name="nodetect" format="fasta" label="No ITS region" from_work_dir="ITSx_out_no_detections.fasta"/>\n+ <data name="positions" format="tabular" label="ITSx feature positions" from_work_dir="ITSx_out.positions.txt"/>\n+ <data name="problematic" format="tabular" label="Problematic sequences" from_work_dir="ITSx_out.problematic.txt"/>\n+ <data name="summary" format="txt" label="ITSx summary" from_work_dir="ITSx_out.summary.txt"/>\n+ <data name="extractions" format="tabular" label="ITSx extraction results" from_work_dir="ITSx_out.extraction.results"/>\n+ </outputs>\n+\n+ <stdio>\n+ <regex match="ITSx" source="both" level="log"/>\n+ <regex match="analysis" source="both" level="log"/>\n+ <regex match="ERROR" source="both" level="fatal"/>\n+ <regex match="error" source="both" level="fatal"/>\n+ </stdio>\n+\n+ <test></test>\n+ <help>\n+ITSx -- Identifies ITS sequences and extracts the ITS region\n+\n+Source code available at:\n+http://microbiology.se/software/itsx\n+\n+Version: 1.0.6\n+ITSx -- Identifies ITS sequences and extracts the ITS region\n+Copyright (C) 2012-2013 Johan Bengtsson-Palme et al.\n+Contact: Johan Bengtsson-Palme, johan[at]microbiology.se\n+Programmer: Johan Bengtsson-Palme\n+\n+Full installation instructions can be found in the User\'s Guide.\n+A quick installation guide follows below.\n+\n+ITSx requires Perl and HMMER3.\n+\n+1) Perl is usually installed on Unix-like systems by default. If not, it can be retrieved from http://www.perl.org/\n+\n+2) HMMER3 can be found at http://hmmer.janelia.org/software\n+Download it and follow the on site instructions for installation.\n+\n+3) Obtain the ITSx package from http://microbiology.se/software/itsx\n+Unpack the tarball and move into the newly created "ITSx" directory.\n+\n+4) Copy the ITSx file and the ITSx_db directory to your preferred bin directory.\n+\n+5) To test if ITSx was successfully installed type "ITSx --help" on the command-line. You should now see the ITSx help message.\n+\n+To run ITSx, you need a FASTA-formatted output file. You can e.g. use the test.fasta file supplied with the package. To check for ITS sequences in the test file, type "ITSx -i test.fasta -o test" on the command line. If you are on a multicore machine, you might want to use the "--cpu 2" option to speed up the processes by using two (or more) cores.\n+'..b"time stamp to the output directory, off (F) by default\n+\n+--reset {T or F} : Re-creates the HMM-database before ITSx is run, off (F) by default\n+\n+Sequence selection options:\n+\n+-t {character code} : Profile set to use for the search, see the User's Guide (comma-separated), default is all\n+\n+-E {value} : Domain E-value cutoff for a sequence to be included in the output, default = 1e-5\n+\n+-S {value} : Domain score cutoff for a sequence to be included in the output, default = 0\n+\n+-N {value} : The minimal number of domains that must match a sequence before it is included, default = 2\n+\n+--selection_priority {sum, domains, eval, score} : Selects what will be of highest priority when determining the origin of the sequence, default is sum\n+\n+--search_eval {value} : The E-value cutoff used in the HMMER search, high numbers may slow down the process, cannot be used with the --search_score option, default is 0.01\n+\n+--search_score {value} : The score cutoff used in the HMMER search, low numbers may slow down the process, cannot be used with the --search_eval option, default is to used E-value cutoff, not score\n+\n+--allow_single_domain {e-value,score or F} : Allow inclusion of sequences that only find a single domain, given that they meet the given E-value and score thresholds, on with parameters 1e-9,0 by default\n+\n+--allow_reorder {T or F} : Allows profiles to be in the wrong order on extracted sequences, off (F) by default\n+\n+--complement {T or F} : Checks both DNA strands against the database, creating reverse complements, on (T) by default\n+\n+--cpu {value} : the number of CPU threads to use, default is 1\n+\n+--multi_thread {T or F} : Multi-thread the HMMER-search, on (T) if number of CPUs (--cpu option > 1), else off (F) by default\n+\n+--heuristics {T or F} : Selects whether to use HMMER's heuristic filtering, off (F) by default\n+\n+Output options:\n+\n+--summary {T or F} : Summary of results output, on (T) by default\n+\n+--graphical {T or F} : 'Graphical' output, on (T) by default\n+\n+--fasta {T or F} : FASTA-format output of extracted ITS sequences, on (T) by default\n+\n+--preserve {T or F} : Preserve sequence headers in input file instead of printing out ITSx headers, off (F) by default\n+\n+--save_regions {SSU,ITS1,5.8S,ITS2,LSU,all,none} : A comma separated list of regions to output separate FASTA files for, 'ITS1,ITS2' by default\n+\n+--anchor {integer or HMM} : Saves an additional number of bases before and after each extracted region. If set to 'HMM' all bases matching the corresponding HMM will be output, default = 0\n+\n+--partial {integer} : Saves additional FASTA-files for full and partial ITS sequences longer than the specified cutoff, default = 0 (off)\n+\n+--concat {T or F} : Saves a FASTA-file with concatenated ITS sequences (with 5.8S removed), off (F) by default\n+\n+--minlen {integer} : Minimum length the ITS regions must be to be outputted in the concatenated file (see above), default = 0\n+\n+--positions {T or F} : Table format output containing the positions ITS sequences were found in, on (T) by default\n+\n+--table {T or F} : Table format output of sequences containing probable ITS sequences, off (F) by default\n+\n+--not_found {T or F} : Saves a list of non-found entries, on (T) by default\n+\n+--detailed_results {T or F} : Saves a tab-separated list of all results, off (F) by default\n+\n+--truncate {T or F} : Truncates the FASTA output to only contain the actual ITS sequences found, on (T) by default\n+\n+--silent {T or F} : Supresses printing progress info to stderr, off (F) by default\n+\n+--graph_scale {value} : Sets the scale of the graph output, if value is zero, a percentage view is shown, default = 0\n+\n+--save_raw {T or F} : Saves all raw data for searches etc. instead of removing it on finish, off (F) by default\n+\n+-h : displays this help message\n+\n+--help : displays this help message\n+\n+--bugs : displays the bug fixes and known bugs in this version of ITSx\n+\n+--license : displays licensing information\n+\n+ </help>\n+\n+</tool>\n" |
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| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/A.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/A.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,13640 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Alveolata_58S_end_eighta_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Wed Feb 29 22:48:49 2012\n+NSEQ 2\n+EFFN 2.000000\n+CKSUM 875354829\n+STATS LOCAL MSV -7.4772 0.72750\n+STATS LOCAL VITERBI -8.4131 0.72750\n+STATS LOCAL FORWARD -3.2493 0.72750\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.02810 1.19053 1.12475 1.42869\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 *\n+ 1 2.53331 3.02441 0.20344 2.88069 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 2 2.53331 3.02441 0.20344 2.88069 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 3 2.81865 0.23582 2.88868 2.35662 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 4 2.53331 3.02441 0.20344 2.88069 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 5 2.81865 0.23582 2.88868 2.35662 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 6 2.81865 0.23582 2.88868 2.35662 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 7 2.53331 3.02441 0.20344 2.88069 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 8 2.57915 2.25909 2.64442 0.28946 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 9 0.23862 2.84929 2.43386 2.70756 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 10 2.81865 0.23582 2.88868 2.35662 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 11 2.53331 3.02441 0.20344 2.88069 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 12 2.53331 3.02441 0.20344 2.88069 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 13 2.57915 2.25909 2.64442 0.28946 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 14 2.57915 2.25909 2.64442 0.28946 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 15 2.81865 0.23582 2.88868 2.35662 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 16 2.53331 3.02441 0.20344 2.88069 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 17 2.81865 0.23582 2.88868 2.35662 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 18 2.81865 0.23582 2.88868 2.35662 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 19 2.53331 3.02441 0.20344 2.88069 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 20 2.57915 2.25909 2.644'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 24 3.10493 2.60552 3.15246 0.17607 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 25 2.95876 3.60411 0.11539 3.51048 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 26 0.13978 3.39641 2.81240 3.29960 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 27 0.13978 3.39641 2.81240 3.29960 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 28 3.45170 0.12801 3.50037 2.84251 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 29 3.45170 0.12801 3.50037 2.84251 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 30 3.10493 2.60552 3.15246 0.17607 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 31 2.95876 3.60411 0.11539 3.51048 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 32 3.45170 0.12801 3.50037 2.84251 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 33 0.13978 3.39641 2.81240 3.29960 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 34 2.95876 3.60411 0.11539 3.51048 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 35 0.13978 3.39641 2.81240 3.29960 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 36 3.10493 2.60552 3.15246 0.17607 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 37 2.95876 3.60411 0.11539 3.51048 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 38 2.95876 3.60411 0.11539 3.51048 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 39 0.13978 3.39641 2.81240 3.29960 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 40 3.10493 2.60552 3.15246 0.17607 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 41 3.45170 0.12801 3.50037 2.84251 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 42 0.13978 3.39641 2.81240 3.29960 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 43 3.10493 2.60552 3.15246 0.17607 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 44 3.10493 2.60552 3.15246 0.17607 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03654 4.02061 4.02061 1.46634 0.26236 1.09861 0.40547\n+ 45 3.45170 0.12801 3.50037 2.84251 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01844 4.00251 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/A.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/A.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/A.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/A.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/A.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/A.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/A.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/A.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/B.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/B.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,2325 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Bryophyta_58S_end_four_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Wed Jan 25 22:55:01 2012\n+NSEQ 32\n+EFFN 3.136719\n+CKSUM 2659440974\n+STATS LOCAL MSV -8.2375 0.71932\n+STATS LOCAL VITERBI -7.5917 0.71932\n+STATS LOCAL FORWARD -3.9020 0.71932\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.72251 1.15807 1.14566 1.66454\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 0.00000 *\n+ 1 3.02702 2.55588 3.07751 0.18893 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 2 2.90418 3.52505 0.12426 3.42332 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 3 3.36220 0.13900 3.41461 2.77708 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 4 2.90418 3.52505 0.12426 3.42332 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 5 3.36220 0.13900 3.41461 2.77708 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 6 3.36220 0.13900 3.41461 2.77708 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 7 3.36220 0.13900 3.41461 2.77708 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 8 2.90418 3.52505 0.12426 3.42332 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 9 0.15028 3.31884 2.76184 3.21476 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 10 2.90418 3.52505 0.12426 3.42332 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 11 2.90418 3.52505 0.12426 3.42332 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 12 3.36220 0.13900 3.41461 2.77708 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 13 3.02702 2.55588 3.07751 0.18893 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 14 3.36220 0.13900 3.41461 2.77708 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 15 2.90418 3.52505 0.12426 3.42332 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 16 0.15028 3.31884 2.76184 3.21476 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 17 3.36220 0.13900 3.41461 2.77708 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 18 3.36220 0.13900 3.41461 2.77708 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 19 2.90418 3.52505 0.12426 3.42332 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03820 3.97720 3.97720 1.46634 0.26236 1.09861 0.40547\n+ 20 0.15028 3.31884 2.7618'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 24 3.10096 2.60299 3.14864 0.17670 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 25 2.95603 3.60014 0.11581 3.50610 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14029 3.39248 2.80985 3.29530 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14029 3.39248 2.80985 3.29530 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 28 3.44718 0.12854 3.49604 2.83923 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 29 3.44718 0.12854 3.49604 2.83923 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 30 3.10096 2.60299 3.14864 0.17670 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 31 2.95603 3.60014 0.11581 3.50610 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 32 3.44718 0.12854 3.49604 2.83923 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 33 2.95603 3.60014 0.11581 3.50610 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 34 2.95603 3.60014 0.11581 3.50610 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14029 3.39248 2.80985 3.29530 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14029 3.39248 2.80985 3.29530 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 37 2.95603 3.60014 0.11581 3.50610 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 38 2.95603 3.60014 0.11581 3.50610 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14029 3.39248 2.80985 3.29530 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 40 3.10096 2.60299 3.14864 0.17670 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 41 3.44718 0.12854 3.49604 2.83923 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14029 3.39248 2.80985 3.29530 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 43 3.10096 2.60299 3.14864 0.17670 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 44 3.10096 2.60299 3.14864 0.17670 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03663 4.01838 4.01838 1.46634 0.26236 1.09861 0.40547\n+ 45 2.95603 3.60014 0.11581 3.50610 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01848 4.00023 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/B.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/B.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/B.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/B.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/B.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/B.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/B.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/B.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/C.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/C.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,3100 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Bacillariophyta_58S_end_eight_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Fri Jan 20 11:42:32 2012\n+NSEQ 5\n+EFFN 3.325195\n+CKSUM 993487011\n+STATS LOCAL MSV -8.1073 0.71931\n+STATS LOCAL VITERBI -7.7843 0.71931\n+STATS LOCAL FORWARD -3.8720 0.71931\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.47720 1.44778 1.45140 1.19603\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 0.00000 *\n+ 1 2.94809 3.58857 0.11707 3.49333 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 2 3.43404 0.13010 3.48346 2.82967 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 3 2.94809 3.58857 0.11707 3.49333 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 4 3.43404 0.13010 3.48346 2.82967 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 5 3.08942 2.59566 3.13755 0.17855 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 6 0.14179 3.38107 2.80245 3.28281 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 7 3.43404 0.13010 3.48346 2.82967 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 8 3.08942 2.59566 3.13755 0.17855 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 9 2.94809 3.58857 0.11707 3.49333 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 10 0.14179 3.38107 2.80245 3.28281 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 11 2.94809 3.58857 0.11707 3.49333 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 12 3.08942 2.59566 3.13755 0.17855 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 13 0.14179 3.38107 2.80245 3.28281 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 14 0.14179 3.38107 2.80245 3.28281 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 15 3.08942 2.59566 3.13755 0.17855 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 16 3.43404 0.13010 3.48346 2.82967 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 17 3.08942 2.59566 3.13755 0.17855 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 18 3.43404 0.13010 3.48346 2.82967 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 19 0.14179 3.38107 2.80245 3.28281 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03687 4.01190 4.01190 1.46634 0.26236 1.09861 0.40547\n+ 20 2.94809 3.58857 0'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05675 2.57485 3.10612 0.18390 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92530 3.55551 0.12075 3.45686 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14615 3.34859 2.78130 3.24727 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14615 3.34859 2.78130 3.24727 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39657 0.13465 3.44756 2.80232 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39657 0.13465 3.44756 2.80232 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05675 2.57485 3.10612 0.18390 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92530 3.55551 0.12075 3.45686 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39657 0.13465 3.44756 2.80232 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92530 3.55551 0.12075 3.45686 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92530 3.55551 0.12075 3.45686 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14615 3.34859 2.78130 3.24727 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14615 3.34859 2.78130 3.24727 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92530 3.55551 0.12075 3.45686 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92530 3.55551 0.12075 3.45686 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14615 3.34859 2.78130 3.24727 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05675 2.57485 3.10612 0.18390 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39657 0.13465 3.44756 2.80232 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14615 3.34859 2.78130 3.24727 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05675 2.57485 3.10612 0.18390 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05675 2.57485 3.10612 0.18390 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14615 3.34859 2.78130 3.24727 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01896 3.97506 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/C.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/C.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/C.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/C.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/C.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/C.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/C.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/C.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/D.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/D.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,3875 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Amoebozoa_58S_end_four_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Fri Jan 20 23:03:49 2012\n+NSEQ 5\n+EFFN 3.198242\n+CKSUM 1352929219\n+STATS LOCAL MSV -8.1195 0.71934\n+STATS LOCAL VITERBI -7.8448 0.71934\n+STATS LOCAL FORWARD -3.8579 0.71934\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.36165 1.09112 1.20867 1.30453\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 0.00000 *\n+ 1 0.14739 3.33958 2.77542 3.23743 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 2 3.38618 0.13595 3.43760 2.79470 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 3 2.91894 3.54631 0.12180 3.44673 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 4 3.04773 2.56910 3.09744 0.18541 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 5 2.91894 3.54631 0.12180 3.44673 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 6 3.38618 0.13595 3.43760 2.79470 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 7 2.91894 3.54631 0.12180 3.44673 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 8 2.91894 3.54631 0.12180 3.44673 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 9 3.38618 0.13595 3.43760 2.79470 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 10 3.38618 0.13595 3.43760 2.79470 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 11 3.04773 2.56910 3.09744 0.18541 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 12 3.38618 0.13595 3.43760 2.79470 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 13 2.91894 3.54631 0.12180 3.44673 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 14 3.04773 2.56910 3.09744 0.18541 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 15 3.38618 0.13595 3.43760 2.79470 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 16 3.04773 2.56910 3.09744 0.18541 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 17 3.04773 2.56910 3.09744 0.18541 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 18 3.38618 0.13595 3.43760 2.79470 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 19 2.91894 3.54631 0.12180 3.44673 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03775 3.98866 3.98866 1.46634 0.26236 1.09861 0.40547\n+ 20 2.91894 3.54631 0.12180'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 24 3.10566 2.60598 3.15316 0.17595 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 25 2.95925 3.60483 0.11531 3.51128 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 26 0.13969 3.39712 2.81286 3.30038 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 27 0.13969 3.39712 2.81286 3.30038 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 28 3.45252 0.12792 3.50115 2.84311 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 29 3.45252 0.12792 3.50115 2.84311 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 30 3.10566 2.60598 3.15316 0.17595 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 31 2.95925 3.60483 0.11531 3.51128 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 32 3.45252 0.12792 3.50115 2.84311 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 33 2.71968 2.72902 0.19871 3.01523 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 34 2.95925 3.60483 0.11531 3.51128 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 35 0.13969 3.39712 2.81286 3.30038 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 36 3.10566 2.60598 3.15316 0.17595 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 37 2.95925 3.60483 0.11531 3.51128 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 38 2.95925 3.60483 0.11531 3.51128 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 39 0.13969 3.39712 2.81286 3.30038 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 40 3.10566 2.60598 3.15316 0.17595 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 41 3.45252 0.12792 3.50115 2.84311 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 42 0.13969 3.39712 2.81286 3.30038 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 43 3.10566 2.60598 3.15316 0.17595 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 44 3.10566 2.60598 3.15316 0.17595 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03653 4.02102 4.02102 1.46634 0.26236 1.09861 0.40547\n+ 45 2.33315 2.44141 2.77551 0.28282 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01843 4.00292 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/D.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/D.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/D.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/D.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/D.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/D.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/D.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/D.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/E.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/E.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,2170 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Euglenozoa_58S_end_five_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Fri Jan 20 21:20:25 2012\n+NSEQ 5\n+EFFN 3.305664\n+CKSUM 1011588078\n+STATS LOCAL MSV -8.1772 0.71930\n+STATS LOCAL VITERBI -7.8656 0.71930\n+STATS LOCAL FORWARD -3.6513 0.71930\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.83104 0.97779 1.32465 1.62094\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 0.00000 *\n+ 1 3.42681 0.13096 3.47654 2.82441 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 2 3.42681 0.13096 3.47654 2.82441 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 3 3.42681 0.13096 3.47654 2.82441 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 4 3.42681 0.13096 3.47654 2.82441 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 5 2.43822 1.17704 2.50879 0.64793 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 6 3.42681 0.13096 3.47654 2.82441 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 7 2.94371 3.58221 0.11777 3.48630 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 8 2.94371 3.58221 0.11777 3.48630 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 9 2.94371 3.58221 0.11777 3.48630 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 10 2.94371 3.58221 0.11777 3.48630 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 11 2.66304 1.70497 2.72642 0.38121 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 12 3.42681 0.13096 3.47654 2.82441 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 13 0.14262 3.37480 2.79837 3.27595 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 14 3.08310 2.59163 3.13146 0.17957 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 15 3.42681 0.13096 3.47654 2.82441 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 16 3.42681 0.13096 3.47654 2.82441 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 17 3.42681 0.13096 3.47654 2.82441 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 18 3.42681 0.13096 3.47654 2.82441 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 19 2.94371 3.58221 0.11777 3.48630 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03700 4.00836 4.00836 1.46634 0.26236 1.09861 0.40547\n+ 20 3.08310 2.59163 3.1314'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 24 0.15719 3.27118 2.73043 3.16274 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 25 3.30705 0.14631 3.36166 2.73626 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 26 3.30705 0.14631 3.36166 2.73626 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 27 2.97980 2.52563 3.03204 0.19727 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 28 2.86982 3.47591 0.13017 3.36931 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 29 3.30705 0.14631 3.36166 2.73626 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 30 0.15719 3.27118 2.73043 3.16274 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 31 2.86982 3.47591 0.13017 3.36931 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 32 3.30705 0.14631 3.36166 2.73626 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 33 0.15719 3.27118 2.73043 3.16274 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 34 2.86982 3.47591 0.13017 3.36931 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 35 3.30705 0.14631 3.36166 2.73626 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 36 2.97980 2.52563 3.03204 0.19727 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 37 2.86982 3.47591 0.13017 3.36931 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 38 2.86982 3.47591 0.13017 3.36931 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 39 0.15719 3.27118 2.73043 3.16274 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 40 2.97980 2.52563 3.03204 0.19727 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 41 3.30705 0.14631 3.36166 2.73626 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 42 0.15719 3.27118 2.73043 3.16274 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 43 2.97980 2.52563 3.03204 0.19727 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 44 2.97980 2.52563 3.03204 0.19727 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03922 3.95124 3.95124 1.46634 0.26236 1.09861 0.40547\n+ 45 2.97980 2.52563 3.03204 0.19727 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01980 3.93183 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/E.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/E.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/E.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/E.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/E.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/E.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/E.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/E.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/F.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/F.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,65255 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Fungi_Ca_58S_end_one_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Tue Feb 7 14:07:35 2012\n+NSEQ 24\n+EFFN 3.272461\n+CKSUM 1239174981\n+STATS LOCAL MSV -8.1718 0.71931\n+STATS LOCAL VITERBI -7.7338 0.71931\n+STATS LOCAL FORWARD -3.5765 0.71931\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.36710 1.94048 0.91540 1.60363\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 0.00000 *\n+ 1 2.93618 3.57128 0.11898 3.47424 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 2 3.07227 2.58474 3.12105 0.18133 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 3 2.93618 3.57128 0.11898 3.47424 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 4 2.93618 3.57128 0.11898 3.47424 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 5 3.41442 0.13246 3.46466 2.81537 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 6 2.93618 3.57128 0.11898 3.47424 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 7 2.93618 3.57128 0.11898 3.47424 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 8 0.14405 3.36405 2.79138 3.26418 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 9 2.93618 3.57128 0.11898 3.47424 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 10 2.93618 3.57128 0.11898 3.47424 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 11 0.14405 3.36405 2.79138 3.26418 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 12 3.07227 2.58474 3.12105 0.18133 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 13 2.93618 3.57128 0.11898 3.47424 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 14 0.14405 3.36405 2.79138 3.26418 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 15 0.14405 3.36405 2.79138 3.26418 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 16 2.93618 3.57128 0.11898 3.47424 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 17 0.14405 3.36405 2.79138 3.26418 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 18 3.41442 0.13246 3.46466 2.81537 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 19 0.14405 3.36405 2.79138 3.26418 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03723 4.00231 4.00231 1.46634 0.26236 1.09861 0.40547\n+ 20 0.14405 3.36405 2.79138'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 24 2.53331 3.02441 0.20344 2.88069 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 25 2.53331 3.02441 0.20344 2.88069 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 26 0.23862 2.84929 2.43386 2.70756 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 27 0.23862 2.84929 2.43386 2.70756 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 28 2.81865 0.23582 2.88868 2.35662 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 29 2.81865 0.23582 2.88868 2.35662 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 30 2.57915 2.25909 2.64442 0.28946 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 31 2.53331 3.02441 0.20344 2.88069 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 32 2.81865 0.23582 2.88868 2.35662 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 33 2.53331 3.02441 0.20344 2.88069 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 34 2.53331 3.02441 0.20344 2.88069 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 35 0.23862 2.84929 2.43386 2.70756 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 36 0.23862 2.84929 2.43386 2.70756 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 37 2.53331 3.02441 0.20344 2.88069 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 38 2.53331 3.02441 0.20344 2.88069 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 39 0.23862 2.84929 2.43386 2.70756 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 40 2.57915 2.25909 2.64442 0.28946 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 41 2.81865 0.23582 2.88868 2.35662 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 42 0.23862 2.84929 2.43386 2.70756 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 43 2.57915 2.25909 2.64442 0.28946 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 44 2.57915 2.25909 2.64442 0.28946 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 45 0.23862 2.84929 2.43386 2.70756 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02469 3.71357 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/F.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/F.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/F.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/F.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/F.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/F.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/F.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/F.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/G.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/G.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,8370 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Chlorophyta_58S_end_eight_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Sat Jan 28 01:06:57 2012\n+NSEQ 8\n+EFFN 3.128906\n+CKSUM 1519682346\n+STATS LOCAL MSV -8.1109 0.71934\n+STATS LOCAL VITERBI -7.7889 0.71934\n+STATS LOCAL FORWARD -3.6308 0.71934\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.06483 0.95712 1.26884 1.57019\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 0.00000 *\n+ 1 3.35912 0.13939 3.41165 2.77481 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 2 2.90228 3.52232 0.12458 3.42031 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 3 3.35912 0.13939 3.41165 2.77481 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 4 3.35912 0.13939 3.41165 2.77481 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 5 3.35912 0.13939 3.41165 2.77481 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 6 3.35912 0.13939 3.41165 2.77481 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 7 0.15066 3.31617 2.76009 3.21184 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 8 3.35912 0.13939 3.41165 2.77481 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 9 2.90228 3.52232 0.12458 3.42031 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 10 2.90228 3.52232 0.12458 3.42031 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 11 3.35912 0.13939 3.41165 2.77481 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 12 3.35912 0.13939 3.41165 2.77481 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 13 3.02437 2.55419 3.07496 0.18939 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 14 3.35912 0.13939 3.41165 2.77481 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 15 2.90228 3.52232 0.12458 3.42031 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 16 2.90228 3.52232 0.12458 3.42031 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 17 3.35912 0.13939 3.41165 2.77481 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 18 3.35912 0.13939 3.41165 2.77481 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 19 3.35912 0.13939 3.41165 2.77481 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03825 3.97573 3.97573 1.46634 0.26236 1.09861 0.40547\n+ 20 0.15066 3.31617 2.76'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05375 2.57294 3.10323 0.18440 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92319 3.55246 0.12110 3.45350 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14656 3.34560 2.77935 3.24400 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14656 3.34560 2.77935 3.24400 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39312 0.13508 3.44425 2.79979 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39312 0.13508 3.44425 2.79979 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05375 2.57294 3.10323 0.18440 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92319 3.55246 0.12110 3.45350 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39312 0.13508 3.44425 2.79979 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92319 3.55246 0.12110 3.45350 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92319 3.55246 0.12110 3.45350 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14656 3.34560 2.77935 3.24400 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14656 3.34560 2.77935 3.24400 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92319 3.55246 0.12110 3.45350 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92319 3.55246 0.12110 3.45350 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14656 3.34560 2.77935 3.24400 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05375 2.57294 3.10323 0.18440 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39312 0.13508 3.44425 2.79979 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14656 3.34560 2.77935 3.24400 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05375 2.57294 3.10323 0.18440 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05375 2.57294 3.10323 0.18440 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03762 3.99200 3.99200 1.46634 0.26236 1.09861 0.40547\n+ 45 2.92319 3.55246 0.12110 3.45350 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01899 3.97336 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/G.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/G.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/G.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/G.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/G.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/G.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/G.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/G.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/H.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/H.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,3720 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Rhodophyta_58S_end_four_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Wed Jan 25 21:56:19 2012\n+NSEQ 2\n+EFFN 2.000000\n+CKSUM 3310020795\n+STATS LOCAL MSV -7.3962 0.72785\n+STATS LOCAL VITERBI -8.3431 0.72785\n+STATS LOCAL FORWARD -3.4147 0.72785\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.39505 1.59495 1.20617 1.38662\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 *\n+ 1 2.53331 3.02441 0.20344 2.88069 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 2 2.81865 0.23582 2.88868 2.35662 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 3 2.53331 3.02441 0.20344 2.88069 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 4 2.81865 0.23582 2.88868 2.35662 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 5 2.57915 2.25909 2.64442 0.28946 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 6 2.81865 0.23582 2.88868 2.35662 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 7 2.57915 2.25909 2.64442 0.28946 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 8 2.81865 0.23582 2.88868 2.35662 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 9 2.53331 3.02441 0.20344 2.88069 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 10 2.53331 3.02441 0.20344 2.88069 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 11 2.53331 3.02441 0.20344 2.88069 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 12 2.57915 2.25909 2.64442 0.28946 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 13 0.23862 2.84929 2.43386 2.70756 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 14 0.23862 2.84929 2.43386 2.70756 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 15 2.57915 2.25909 2.64442 0.28946 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 16 2.81865 0.23582 2.88868 2.35662 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 17 2.81865 0.23582 2.88868 2.35662 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 18 2.57915 2.25909 2.64442 0.28946 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 19 2.53331 3.02441 0.20344 2.88069 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 20 2.53331 3.02441 0.2034'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 24 3.41129 0.13284 3.46167 2.81309 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 25 0.14442 3.36134 2.78962 3.26122 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 26 3.06955 2.58301 3.11843 0.18178 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 27 2.93428 3.56852 0.11929 3.47120 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 28 3.06955 2.58301 3.11843 0.18178 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 29 3.41129 0.13284 3.46167 2.81309 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 30 3.06955 2.58301 3.11843 0.18178 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 31 2.93428 3.56852 0.11929 3.47120 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 32 3.06955 2.58301 3.11843 0.18178 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 33 3.06955 2.58301 3.11843 0.18178 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 34 3.06955 2.58301 3.11843 0.18178 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 35 2.93428 3.56852 0.11929 3.47120 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14442 3.36134 2.78962 3.26122 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 37 2.93428 3.56852 0.11929 3.47120 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 38 3.06955 2.58301 3.11843 0.18178 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 39 2.93428 3.56852 0.11929 3.47120 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 40 3.06955 2.58301 3.11843 0.18178 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 41 3.41129 0.13284 3.46167 2.81309 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14442 3.36134 2.78962 3.26122 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 43 3.41129 0.13284 3.46167 2.81309 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 44 3.06955 2.58301 3.11843 0.18178 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03729 4.00080 4.00080 1.46634 0.26236 1.09861 0.40547\n+ 45 3.06955 2.58301 3.11843 0.18178 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01882 3.98232 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/H.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/H.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/H.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/H.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/H.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/H.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/H.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/H.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/I.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/I.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,775 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Phaeophyceae_58S_end_one_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Fri Jan 20 12:12:36 2012\n+NSEQ 157\n+EFFN 3.732391\n+CKSUM 82106143\n+STATS LOCAL MSV -6.9907 0.71931\n+STATS LOCAL VITERBI -7.6013 0.71931\n+STATS LOCAL FORWARD -3.9860 0.71931\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.91751 1.41520 1.11917 1.26019\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 0.00000 *\n+ 1 3.57378 0.11461 3.61706 2.93034 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 2 3.03127 3.71067 0.10455 3.62844 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 3 3.57378 0.11461 3.61706 2.93034 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 4 3.21417 2.67481 3.25746 0.15969 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 5 3.21417 2.67481 3.25746 0.15969 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 6 3.57378 0.11461 3.61706 2.93034 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 7 3.57378 0.11461 3.61706 2.93034 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 8 3.03127 3.71067 0.10455 3.62844 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 9 3.03127 3.71067 0.10455 3.62844 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 10 3.03127 3.71067 0.10455 3.62844 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04253 4.08301 3.69765 1.46634 0.26236 1.09861 0.40547\n+ 11 0.15619 3.32897 2.80495 3.03107 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03457 4.07506 4.07506 1.46634 0.26236 0.85884 0.55105\n+ 12 1.83744 2.35418 2.56143 0.40256 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 13 0.12671 3.50290 2.88107 3.41642 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 14 2.61652 1.41576 2.68268 0.48480 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 15 2.01308 1.45171 1.26036 1.05354 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 16 3.57378 0.11461 3.61706 2.93034 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 17 3.57378 0.11461 3.61706 2.93034 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 18 3.14605 2.49866 3.19205 0.18189 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 19 3.03127 3.71067 0.10455 3.62844 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03429 4.08301 4.08301 1.46634 0.26236 1.09861 0.40547\n+ 20 3.03127 3.71067 0.1045'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05809 2.57571 3.10741 0.18367 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92625 3.55688 0.12059 3.45837 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14597 3.34993 2.78218 3.24874 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14597 3.34993 2.78218 3.24874 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39812 0.13446 3.44905 2.80346 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39812 0.13446 3.44905 2.80346 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05809 2.57571 3.10741 0.18367 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92625 3.55688 0.12059 3.45837 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39812 0.13446 3.44905 2.80346 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92625 3.55688 0.12059 3.45837 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92625 3.55688 0.12059 3.45837 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14597 3.34993 2.78218 3.24874 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14597 3.34993 2.78218 3.24874 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92625 3.55688 0.12059 3.45837 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92625 3.55688 0.12059 3.45837 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14597 3.34993 2.78218 3.24874 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05809 2.57571 3.10741 0.18367 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39812 0.13446 3.44905 2.80346 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14597 3.34993 2.78218 3.24874 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05809 2.57571 3.10741 0.18367 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05809 2.57571 3.10741 0.18367 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99441 3.99441 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14597 3.34993 2.78218 3.24874 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01894 3.97582 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/I.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/I.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/I.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/I.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/I.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/I.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/I.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/I.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/L.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/L.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,6045 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Marchantiophyta_58S_end_foura_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Wed Jan 25 17:48:18 2012\n+NSEQ 4\n+EFFN 3.089844\n+CKSUM 3677159024\n+STATS LOCAL MSV -8.1113 0.71933\n+STATS LOCAL VITERBI -7.8119 0.71933\n+STATS LOCAL FORWARD -3.9220 0.71933\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.72586 1.10743 1.14821 1.74657\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 0.00000 *\n+ 1 3.34359 0.14142 3.39674 2.76335 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 2 2.89265 3.50850 0.12621 3.40512 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 3 3.34359 0.14142 3.39674 2.76335 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 4 3.34359 0.14142 3.39674 2.76335 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 5 3.34359 0.14142 3.39674 2.76335 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 6 2.89265 3.50850 0.12621 3.40512 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 7 0.15258 3.30274 2.75126 3.19718 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 8 2.89265 3.50850 0.12621 3.40512 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 9 2.89265 3.50850 0.12621 3.40512 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 10 3.01102 2.54565 3.06211 0.19171 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 11 3.34359 0.14142 3.39674 2.76335 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 12 3.01102 2.54565 3.06211 0.19171 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 13 3.34359 0.14142 3.39674 2.76335 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 14 2.89265 3.50850 0.12621 3.40512 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 15 3.01102 2.54565 3.06211 0.19171 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 16 0.15258 3.30274 2.75126 3.19718 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 17 3.34359 0.14142 3.39674 2.76335 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 18 3.34359 0.14142 3.39674 2.76335 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 19 2.89265 3.50850 0.12621 3.40512 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03854 3.96837 3.96837 1.46634 0.26236 1.09861 0.40547\n+ 20 0.15258 3.30274 '..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05756 2.57537 3.10690 0.18376 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92588 3.55634 0.12065 3.45778 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14604 3.34940 2.78183 3.24816 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14604 3.34940 2.78183 3.24816 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39751 0.13454 3.44846 2.80301 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39751 0.13454 3.44846 2.80301 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05756 2.57537 3.10690 0.18376 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92588 3.55634 0.12065 3.45778 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39751 0.13454 3.44846 2.80301 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92588 3.55634 0.12065 3.45778 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92588 3.55634 0.12065 3.45778 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14604 3.34940 2.78183 3.24816 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14604 3.34940 2.78183 3.24816 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92588 3.55634 0.12065 3.45778 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92588 3.55634 0.12065 3.45778 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14604 3.34940 2.78183 3.24816 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05756 2.57537 3.10690 0.18376 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39751 0.13454 3.44846 2.80301 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14604 3.34940 2.78183 3.24816 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05756 2.57537 3.10690 0.18376 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05756 2.57537 3.10690 0.18376 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03754 3.99412 3.99412 1.46634 0.26236 1.09861 0.40547\n+ 45 2.92588 3.55634 0.12065 3.45778 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01895 3.97552 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/L.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/L.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/L.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/L.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/L.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/L.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/L.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/L.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/M.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/M.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,54870 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Metazoa_58S_end_eight_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Sat Feb 25 14:35:27 2012\n+NSEQ 2\n+EFFN 2.000000\n+CKSUM 2003464747\n+STATS LOCAL MSV -7.3950 0.72793\n+STATS LOCAL VITERBI -8.3145 0.72793\n+STATS LOCAL FORWARD -3.2953 0.72793\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.58596 1.45659 1.21394 1.32730\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 *\n+ 1 2.57915 2.25909 2.64442 0.28946 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 2 2.81865 0.23582 2.88868 2.35662 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 3 0.23862 2.84929 2.43386 2.70756 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 4 2.53331 3.02441 0.20344 2.88069 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 5 2.53331 3.02441 0.20344 2.88069 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 6 0.23862 2.84929 2.43386 2.70756 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 7 2.81865 0.23582 2.88868 2.35662 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 8 2.81865 0.23582 2.88868 2.35662 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 9 0.23862 2.84929 2.43386 2.70756 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 10 0.23862 2.84929 2.43386 2.70756 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 11 2.57915 2.25909 2.64442 0.28946 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 12 0.23862 2.84929 2.43386 2.70756 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 13 0.23862 2.84929 2.43386 2.70756 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 14 2.57915 2.25909 2.64442 0.28946 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 15 2.57915 2.25909 2.64442 0.28946 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 16 2.81865 0.23582 2.88868 2.35662 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 17 2.81865 0.23582 2.88868 2.35662 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 18 2.57915 2.25909 2.64442 0.28946 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 19 2.53331 3.02441 0.20344 2.88069 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 20 2.81865 0.23582 2.88868'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 24 3.12118 2.61584 3.16808 0.17352 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 25 2.96982 3.62027 0.11366 3.52834 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 26 0.13772 3.41241 2.82276 3.31713 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 27 0.13772 3.41241 2.82276 3.31713 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 28 3.47011 0.12588 3.51799 2.85586 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 29 3.47011 0.12588 3.51799 2.85586 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 30 3.12118 2.61584 3.16808 0.17352 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 31 2.96982 3.62027 0.11366 3.52834 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 32 3.47011 0.12588 3.51799 2.85586 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 33 2.13519 2.26919 2.09248 0.42312 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 34 2.96982 3.62027 0.11366 3.52834 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 35 3.47011 0.12588 3.51799 2.85586 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 36 2.10812 1.99792 2.53146 0.41042 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 37 2.96982 3.62027 0.11366 3.52834 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 38 2.96982 3.62027 0.11366 3.52834 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 39 0.13772 3.41241 2.82276 3.31713 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 40 3.12118 2.61584 3.16808 0.17352 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 41 3.47011 0.12588 3.51799 2.85586 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 42 0.13772 3.41241 2.82276 3.31713 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 43 2.97957 2.28186 3.03175 0.22457 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 44 3.12118 2.61584 3.16808 0.17352 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03620 4.02977 4.02977 1.46634 0.26236 1.09861 0.40547\n+ 45 0.13772 3.41241 2.82276 3.31713 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01827 4.01183 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/M.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/M.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/M.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/M.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/M.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/M.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/M.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/M.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/O.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/O.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,11005 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Oomycota_58S_end_eight_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Mon Jan 23 23:03:14 2012\n+NSEQ 2983\n+EFFN 3.376790\n+CKSUM 630809808\n+STATS LOCAL MSV -7.3235 0.71932\n+STATS LOCAL VITERBI -7.7268 0.71932\n+STATS LOCAL FORWARD -3.9994 0.71932\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.71234 1.37658 1.27028 1.25049\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 0.00000 *\n+ 1 3.45287 0.12788 3.50149 2.84336 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 2 0.13965 3.39742 2.81306 3.30071 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 3 3.45287 0.12788 3.50149 2.84336 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 4 3.10596 2.60617 3.15345 0.17590 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 5 3.07064 2.51740 3.11930 0.18784 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 6 3.40266 0.13843 3.45273 2.74368 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 7 3.45287 0.12788 3.50149 2.84336 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 8 2.95946 3.60514 0.11528 3.51162 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 9 2.95946 3.60514 0.11528 3.51162 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 10 2.95946 3.60514 0.11528 3.51162 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 11 3.07576 2.52995 3.12424 0.18607 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 12 3.10596 2.60617 3.15345 0.17590 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 13 0.13965 3.39742 2.81306 3.30071 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 14 2.95946 3.60514 0.11528 3.51162 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 15 3.01261 2.38100 3.06343 0.20868 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 16 3.45287 0.12788 3.50149 2.84336 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 17 3.45287 0.12788 3.50149 2.84336 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 18 3.10596 2.60617 3.15345 0.17590 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 19 2.95946 3.60514 0.11528 3.51162 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03652 4.02119 4.02119 1.46634 0.26236 1.09861 0.40547\n+ 20 2.95946 3.60514 0.11'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 24 3.07459 2.58622 3.12328 0.18095 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 25 2.93780 3.57362 0.11872 3.47683 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14375 3.36635 2.79288 3.26670 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14375 3.36635 2.79288 3.26670 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05071 4.00361 3.46743 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39016 0.13545 3.44142 2.79762 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03768 3.99057 3.99057 1.46634 0.26236 0.77471 0.61774\n+ 29 3.41707 0.13214 3.46721 2.81731 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 30 3.07459 2.58622 3.12328 0.18095 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 31 2.93780 3.57362 0.11872 3.47683 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 32 3.41707 0.13214 3.46721 2.81731 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 33 2.93780 3.57362 0.11872 3.47683 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 34 2.93780 3.57362 0.11872 3.47683 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14375 3.36635 2.79288 3.26670 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14375 3.36635 2.79288 3.26670 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 37 2.93780 3.57362 0.11872 3.47683 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 38 2.93780 3.57362 0.11872 3.47683 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14375 3.36635 2.79288 3.26670 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 40 3.07459 2.58622 3.12328 0.18095 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 41 3.41707 0.13214 3.46721 2.81731 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14375 3.36635 2.79288 3.26670 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 43 3.07459 2.58622 3.12328 0.18095 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 44 3.07459 2.58622 3.12328 0.18095 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03718 4.00361 4.00361 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14375 3.36635 2.79288 3.26670 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01876 3.98519 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/O.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/O.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/O.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/O.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/O.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/O.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/O.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/O.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/P.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/P.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,1550 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Haptophyceae_58S_end_five_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Thu Jan 19 21:11:03 2012\n+NSEQ 2\n+EFFN 2.000000\n+CKSUM 2494581836\n+STATS LOCAL MSV -7.5772 0.72779\n+STATS LOCAL VITERBI -8.4466 0.72779\n+STATS LOCAL FORWARD -3.4217 0.72779\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.83092 1.23370 1.22080 1.37229\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 *\n+ 1 2.81865 0.23582 2.88868 2.35662 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 2 2.53331 3.02441 0.20344 2.88069 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 3 2.81865 0.23582 2.88868 2.35662 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 4 2.57915 2.25909 2.64442 0.28946 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 5 2.57915 2.25909 2.64442 0.28946 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 6 2.57915 2.25909 2.64442 0.28946 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 7 2.53331 3.02441 0.20344 2.88069 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 8 2.57915 2.25909 2.64442 0.28946 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 9 2.53331 3.02441 0.20344 2.88069 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 10 2.53331 3.02441 0.20344 2.88069 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 11 2.81865 0.23582 2.88868 2.35662 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 12 2.57915 2.25909 2.64442 0.28946 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 13 2.81865 0.23582 2.88868 2.35662 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 14 2.81865 0.23582 2.88868 2.35662 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 15 2.53331 3.02441 0.20344 2.88069 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 16 2.81865 0.23582 2.88868 2.35662 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 17 2.81865 0.23582 2.88868 2.35662 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 18 2.53331 3.02441 0.20344 2.88069 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 19 2.81865 0.23582 2.88868 2.35662 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 20 2.53331 3.02441 0.20'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05675 2.57485 3.10612 0.18390 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92530 3.55551 0.12075 3.45686 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14615 3.34859 2.78130 3.24727 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14615 3.34859 2.78130 3.24727 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39657 0.13465 3.44756 2.80232 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39657 0.13465 3.44756 2.80232 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05675 2.57485 3.10612 0.18390 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92530 3.55551 0.12075 3.45686 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39657 0.13465 3.44756 2.80232 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92530 3.55551 0.12075 3.45686 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92530 3.55551 0.12075 3.45686 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14615 3.34859 2.78130 3.24727 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14615 3.34859 2.78130 3.24727 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92530 3.55551 0.12075 3.45686 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92530 3.55551 0.12075 3.45686 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14615 3.34859 2.78130 3.24727 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05675 2.57485 3.10612 0.18390 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39657 0.13465 3.44756 2.80232 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14615 3.34859 2.78130 3.24727 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05675 2.57485 3.10612 0.18390 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05675 2.57485 3.10612 0.18390 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99367 3.99367 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14615 3.34859 2.78130 3.24727 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01896 3.97506 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/P.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/P.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/P.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/P.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/P.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/P.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/P.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/P.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/Q.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/Q.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,1085 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Raphidophyceae_58S_end_one_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Thu Jan 19 22:28:09 2012\n+NSEQ 29\n+EFFN 3.345337\n+CKSUM 2540392139\n+STATS LOCAL MSV -8.0627 0.71933\n+STATS LOCAL VITERBI -7.5685 0.71933\n+STATS LOCAL FORWARD -3.8000 0.71933\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.72491 1.59887 1.25392 1.09570\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 0.00000 *\n+ 1 3.44143 0.12922 3.49054 2.83505 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 2 0.14094 3.38749 2.80662 3.28984 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 3 3.44143 0.12922 3.49054 2.83505 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 4 3.09591 2.59978 3.14378 0.17750 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 5 3.09591 2.59978 3.14378 0.17750 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 6 3.44143 0.12922 3.49054 2.83505 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 7 3.44143 0.12922 3.49054 2.83505 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 8 2.95256 3.59508 0.11636 3.50051 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 9 2.95256 3.59508 0.11636 3.50051 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 10 2.95256 3.59508 0.11636 3.50051 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 11 0.14094 3.38749 2.80662 3.28984 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 12 3.09591 2.59978 3.14378 0.17750 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 13 0.14094 3.38749 2.80662 3.28984 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 14 3.09591 2.59978 3.14378 0.17750 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 15 3.09591 2.59978 3.14378 0.17750 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 16 3.44143 0.12922 3.49054 2.83505 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 17 3.44143 0.12922 3.49054 2.83505 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 18 3.09591 2.59978 3.14378 0.17750 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 19 2.95256 3.59508 0.11636 3.50051 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03673 4.01554 4.01554 1.46634 0.26236 1.09861 0.40547\n+ 20 2.95256 3.59508 0.'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05845 2.57594 3.10775 0.18362 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92650 3.55724 0.12055 3.45877 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14592 3.35028 2.78241 3.24912 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14592 3.35028 2.78241 3.24912 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39853 0.13441 3.44944 2.80375 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39853 0.13441 3.44944 2.80375 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05845 2.57594 3.10775 0.18362 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92650 3.55724 0.12055 3.45877 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39853 0.13441 3.44944 2.80375 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92650 3.55724 0.12055 3.45877 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92650 3.55724 0.12055 3.45877 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14592 3.35028 2.78241 3.24912 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14592 3.35028 2.78241 3.24912 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92650 3.55724 0.12055 3.45877 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92650 3.55724 0.12055 3.45877 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14592 3.35028 2.78241 3.24912 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05845 2.57594 3.10775 0.18362 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39853 0.13441 3.44944 2.80375 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14592 3.35028 2.78241 3.24912 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05845 2.57594 3.10775 0.18362 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05845 2.57594 3.10775 0.18362 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03752 3.99461 3.99461 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14592 3.35028 2.78241 3.24912 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01894 3.97602 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/Q.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/Q.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/Q.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/Q.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/Q.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/Q.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/Q.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/Q.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/R.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/R.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,6355 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Rhizaria_58S_end_eight_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Fri Jan 20 15:33:02 2012\n+NSEQ 2\n+EFFN 2.000000\n+CKSUM 1899220078\n+STATS LOCAL MSV -7.5314 0.72773\n+STATS LOCAL VITERBI -8.2053 0.72773\n+STATS LOCAL FORWARD -3.4398 0.72773\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.39561 1.53003 1.21055 1.43652\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 0.00000 *\n+ 1 2.57915 2.25909 2.64442 0.28946 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 2 2.81865 0.23582 2.88868 2.35662 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 3 2.57915 2.25909 2.64442 0.28946 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 4 0.23862 2.84929 2.43386 2.70756 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 5 2.57915 2.25909 2.64442 0.28946 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 6 2.57915 2.25909 2.64442 0.28946 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 7 2.81865 0.23582 2.88868 2.35662 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 8 2.57915 2.25909 2.64442 0.28946 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 9 2.81865 0.23582 2.88868 2.35662 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 10 2.81865 0.23582 2.88868 2.35662 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 11 0.23862 2.84929 2.43386 2.70756 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 12 0.23862 2.84929 2.43386 2.70756 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 13 2.81865 0.23582 2.88868 2.35662 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 14 0.23862 2.84929 2.43386 2.70756 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 15 2.53331 3.02441 0.20344 2.88069 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 16 2.53331 3.02441 0.20344 2.88069 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 17 0.23862 2.84929 2.43386 2.70756 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 18 0.23862 2.84929 2.43386 2.70756 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 19 2.57915 2.25909 2.64442 0.28946 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 20 0.23862 2.84929 2.43386'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 24 3.06506 2.58015 3.11411 0.18252 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 25 2.93114 3.56396 0.11980 3.46618 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14502 3.35687 2.78670 3.25633 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14502 3.35687 2.78670 3.25633 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 28 3.40613 0.13347 3.45673 2.80932 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 29 3.40613 0.13347 3.45673 2.80932 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 30 3.06506 2.58015 3.11411 0.18252 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 31 2.93114 3.56396 0.11980 3.46618 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 32 3.40613 0.13347 3.45673 2.80932 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 33 2.93114 3.56396 0.11980 3.46618 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 34 2.93114 3.56396 0.11980 3.46618 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14502 3.35687 2.78670 3.25633 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14502 3.35687 2.78670 3.25633 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 37 2.93114 3.56396 0.11980 3.46618 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 38 2.93114 3.56396 0.11980 3.46618 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14502 3.35687 2.78670 3.25633 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 40 3.06506 2.58015 3.11411 0.18252 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 41 3.40613 0.13347 3.45673 2.80932 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14502 3.35687 2.78670 3.25633 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 43 3.06506 2.58015 3.11411 0.18252 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 44 3.06506 2.58015 3.11411 0.18252 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03738 3.99829 3.99829 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14502 3.35687 2.78670 3.25633 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01887 3.97977 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/R.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/R.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/R.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/R.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/R.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/R.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/R.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/R.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/S.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/S.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,1240 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Synurophyceae_58S_end_one_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Thu Jan 19 22:10:37 2012\n+NSEQ 114\n+EFFN 3.336365\n+CKSUM 556246054\n+STATS LOCAL MSV -7.9476 0.71931\n+STATS LOCAL VITERBI -7.6935 0.71931\n+STATS LOCAL FORWARD -4.0189 0.71931\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.82422 1.38641 1.25673 1.19039\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 0.00000 *\n+ 1 3.43814 0.12961 3.48739 2.83266 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 2 2.95057 3.59219 0.11668 3.49732 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 3 3.43814 0.12961 3.48739 2.83266 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 4 0.14132 3.38463 2.80476 3.28671 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 5 3.09302 2.59795 3.14101 0.17797 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 6 3.43814 0.12961 3.48739 2.83266 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 7 3.09302 2.59795 3.14101 0.17797 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 8 3.09302 2.59795 3.14101 0.17797 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 9 2.95057 3.59219 0.11668 3.49732 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 10 3.43814 0.12961 3.48739 2.83266 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 11 0.14132 3.38463 2.80476 3.28671 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 12 3.43814 0.12961 3.48739 2.83266 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 13 3.09302 2.59795 3.14101 0.17797 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 14 2.95057 3.59219 0.11668 3.49732 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 15 3.43814 0.12961 3.48739 2.83266 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 16 3.43814 0.12961 3.48739 2.83266 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 17 3.09302 2.59795 3.14101 0.17797 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 18 2.93904 0.27285 3.00266 1.99347 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 19 2.95057 3.59219 0.11668 3.49732 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01392 4.01392 1.46634 0.26236 1.09861 0.40547\n+ 20 2.95057 3.59219 0.1'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05815 2.57575 3.10747 0.18366 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92629 3.55695 0.12059 3.45844 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14596 3.34999 2.78222 3.24880 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14596 3.34999 2.78222 3.24880 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39819 0.13445 3.44912 2.80351 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39819 0.13445 3.44912 2.80351 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05815 2.57575 3.10747 0.18366 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92629 3.55695 0.12059 3.45844 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39819 0.13445 3.44912 2.80351 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92629 3.55695 0.12059 3.45844 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92629 3.55695 0.12059 3.45844 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14596 3.34999 2.78222 3.24880 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14596 3.34999 2.78222 3.24880 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92629 3.55695 0.12059 3.45844 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92629 3.55695 0.12059 3.45844 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14596 3.34999 2.78222 3.24880 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05815 2.57575 3.10747 0.18366 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39819 0.13445 3.44912 2.80351 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14596 3.34999 2.78222 3.24880 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05815 2.57575 3.10747 0.18366 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05815 2.57575 3.10747 0.18366 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03753 3.99445 3.99445 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14596 3.34999 2.78222 3.24880 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01894 3.97586 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/S.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/S.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/S.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/S.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/S.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/S.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/S.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/S.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/T.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/T.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,34720 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Tracheophyta_58S_end_eight_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Sat Feb 18 00:57:06 2012\n+NSEQ 662\n+EFFN 4.649132\n+CKSUM 878970887\n+STATS LOCAL MSV -6.9557 0.71932\n+STATS LOCAL VITERBI -7.5350 0.71932\n+STATS LOCAL FORWARD -3.7755 0.71932\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.86570 1.07040 1.08935 1.79633\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 0.00000 *\n+ 1 3.17620 3.92530 0.08600 3.86688 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 2 3.82361 0.09186 3.85519 3.10671 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 3 3.82361 0.09186 3.85519 3.10671 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 4 3.57901 0.14044 3.62229 2.57183 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 5 1.93587 1.39029 0.83718 1.75004 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 6 0.10359 3.72520 3.02434 3.66086 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 7 0.19844 3.34834 2.27973 3.15742 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 8 3.17620 3.92530 0.08600 3.86688 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 9 3.82361 0.09186 3.85519 3.10671 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 10 3.77465 0.10089 3.80859 2.97902 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 11 0.84316 2.18097 1.68775 1.30274 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 12 3.24031 2.25577 3.28501 0.20014 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 13 2.81050 1.42383 2.87304 0.44238 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 14 1.22032 1.28525 1.91165 1.27137 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 15 3.17620 3.92530 0.08600 3.86688 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 16 3.17620 3.92530 0.08600 3.86688 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 17 3.55653 0.14545 3.60081 2.53166 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 18 3.35052 0.19783 3.40305 2.19688 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 19 2.73063 3.76185 0.12042 3.68745 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02964 4.22671 4.22671 1.46634 0.26236 1.09861 0.40547\n+ 20 0.10359 3.72520 3'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 24 2.57915 2.25909 2.64442 0.28946 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 25 2.53331 3.02441 0.20344 2.88069 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 26 0.23862 2.84929 2.43386 2.70756 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 27 0.23862 2.84929 2.43386 2.70756 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 28 2.81865 0.23582 2.88868 2.35662 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 29 2.81865 0.23582 2.88868 2.35662 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 30 2.57915 2.25909 2.64442 0.28946 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 31 2.53331 3.02441 0.20344 2.88069 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 32 2.81865 0.23582 2.88868 2.35662 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 33 2.53331 3.02441 0.20344 2.88069 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 34 2.53331 3.02441 0.20344 2.88069 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 35 0.23862 2.84929 2.43386 2.70756 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 36 0.23862 2.84929 2.43386 2.70756 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 37 2.53331 3.02441 0.20344 2.88069 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 38 2.53331 3.02441 0.20344 2.88069 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 39 0.23862 2.84929 2.43386 2.70756 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 40 2.57915 2.25909 2.64442 0.28946 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 41 2.81865 0.23582 2.88868 2.35662 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 42 0.23862 2.84929 2.43386 2.70756 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 43 2.57915 2.25909 2.64442 0.28946 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 44 2.57915 2.25909 2.64442 0.28946 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04879 3.73767 3.73767 1.46634 0.26236 1.09861 0.40547\n+ 45 2.53331 3.02441 0.20344 2.88069 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02469 3.71357 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/T.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/T.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/T.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/T.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/T.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/T.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/T.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/T.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/U.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ITSx_db/HMMs/U.hmm Tue Mar 24 12:02:48 2015 -0400 |
| [ |
| b'@@ -0,0 +1,620 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME 3_End_Eustigmatophyceae_58S_end_long\n+LENG 45\n+ALPH DNA\n+RF no\n+CS no\n+MAP yes\n+DATE Sun Sep 25 01:39:32 2011\n+NSEQ 6\n+EFFN 3.336914\n+CKSUM 3393550359\n+STATS LOCAL MSV -8.0163 0.71932\n+STATS LOCAL VITERBI -7.6944 0.71932\n+STATS LOCAL FORWARD -4.0151 0.71932\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.93226 1.59605 1.19721 1.04854\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 0.00000 *\n+ 1 3.43835 0.12958 3.48758 2.83281 1 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 2 2.95070 3.59237 0.11666 3.49752 2 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 3 3.43835 0.12958 3.48758 2.83281 3 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 4 3.09320 2.59806 3.14118 0.17794 4 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 5 3.09320 2.59806 3.14118 0.17794 5 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 6 3.09320 2.59806 3.14118 0.17794 6 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 7 3.43835 0.12958 3.48758 2.83281 7 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 8 2.95070 3.59237 0.11666 3.49752 8 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 9 2.95070 3.59237 0.11666 3.49752 9 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 10 2.95070 3.59237 0.11666 3.49752 10 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 11 0.14130 3.38481 2.80488 3.28690 11 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 12 3.09320 2.59806 3.14118 0.17794 12 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 13 0.14130 3.38481 2.80488 3.28690 13 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 14 3.09320 2.59806 3.14118 0.17794 14 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 15 2.95070 3.59237 0.11666 3.49752 15 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 16 3.43835 0.12958 3.48758 2.83281 16 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 17 3.43835 0.12958 3.48758 2.83281 17 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 18 3.43835 0.12958 3.48758 2.83281 18 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 19 2.95070 3.59237 0.11666 3.49752 19 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03679 4.01402 4.01402 1.46634 0.26236 1.09861 0.40547\n+ 20 3.09320 2.59806 3.141'..b'- -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 24 3.05683 2.57491 3.10619 0.18389 24 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 25 2.92536 3.55560 0.12074 3.45696 25 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 26 0.14614 3.34867 2.78135 3.24736 26 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 27 0.14614 3.34867 2.78135 3.24736 27 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 28 3.39667 0.13464 3.44765 2.80239 28 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 29 3.39667 0.13464 3.44765 2.80239 29 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 30 3.05683 2.57491 3.10619 0.18389 30 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 31 2.92536 3.55560 0.12074 3.45696 31 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 32 3.39667 0.13464 3.44765 2.80239 32 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 33 2.92536 3.55560 0.12074 3.45696 33 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 34 2.92536 3.55560 0.12074 3.45696 34 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 35 0.14614 3.34867 2.78135 3.24736 35 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 36 0.14614 3.34867 2.78135 3.24736 36 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 37 2.92536 3.55560 0.12074 3.45696 37 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 38 2.92536 3.55560 0.12074 3.45696 38 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 39 0.14614 3.34867 2.78135 3.24736 39 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 40 3.05683 2.57491 3.10619 0.18389 40 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 41 3.39667 0.13464 3.44765 2.80239 41 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 42 0.14614 3.34867 2.78135 3.24736 42 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 43 3.05683 2.57491 3.10619 0.18389 43 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 44 3.05683 2.57491 3.10619 0.18389 44 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03756 3.99371 3.99371 1.46634 0.26236 1.09861 0.40547\n+ 45 0.14614 3.34867 2.78135 3.24736 45 - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01896 3.97511 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/U.hmm.h3f |
| b |
| Binary file ITSx_db/HMMs/U.hmm.h3f has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/U.hmm.h3i |
| b |
| Binary file ITSx_db/HMMs/U.hmm.h3i has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/U.hmm.h3m |
| b |
| Binary file ITSx_db/HMMs/U.hmm.h3m has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 ITSx_db/HMMs/U.hmm.h3p |
| b |
| Binary file ITSx_db/HMMs/U.hmm.h3p has changed |
| b |
| diff -r 000000000000 -r f82c70f54bd7 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Mar 24 12:02:48 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="hmmer" version="3.1b1"> + <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |