|
Commit message:
planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty |
|
added:
DNAconvert DNAconvert.xml README.md test-data/DNAconvert_examplefile2_iTaxoTools_0_1.fas test-data/DNAconvert_examplefile3_iTaxoTools_0_1.tab test-data/DNAtestout_1.tab test-data/DNAtestout_2.phy |
| b |
| diff -r 000000000000 -r aef9a0c2c65e DNAconvert |
| b |
| Binary file DNAconvert has changed |
| b |
| diff -r 000000000000 -r aef9a0c2c65e DNAconvert.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DNAconvert.xml Sun Jan 29 16:32:28 2023 +0000 |
| [ |
| b'@@ -0,0 +1,184 @@\n+<tool id="DNAconvert" name="DNAconvert" version="0.2.0" python_template_version="3.5" profile="21.05">\r\n+ <description>Converts genetic sequences between different formats</description>\r\n+ <requirements>\r\n+ </requirements>\r\n+ <command detect_errors="exit_code"><![CDATA[$__tool_directory__/DNAconvert \'$input1\' \'$output1\' \'--cmd\' \r\n+ #if $allow_empty_sequences: \r\n+ --allow_empty_sequence \r\n+ #end if\r\n+ #if $disable_automatic_renaming: \r\n+ --disable_automatic_renaming\r\n+ #end if\r\n+ --informat \'$informat1\'\r\n+\t --outformat \'$outformat_and_extension.outformat1\' ]]>\r\n+ </command>\r\n+ <inputs>\r\n+ <param type="data" name="input1" label="Source file" format="data" />\r\n+ <param name="informat1" type="select" label="Input Format">\r\n+ <option value="tab">Internal tab format</option>\r\n+ <option value="tab_noheaders">Internal tab format without headers</option>\r\n+ <option value="fasta">FASTA format</option>\r\n+ <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>\r\n+ <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>\r\n+ <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>\r\n+ <option value="fastq">FASTQ format</option>\r\n+ <option value="phylip">Phylip format</option>\r\n+ <option value="relaxed_phylip">relaxed Phylip format</option>\r\n+ <option value="nexus">NEXUS format</option>\r\n+ <option value="nexml">DnaCharacterMatrix in NeXML format</option>\r\n+ <option value="genbank">Genbank flat file format</option>\r\n+ </param>\r\n+ <conditional name="outformat_and_extension">\r\n+ <param name="outformat1" type="select" label="Output Format">\r\n+ <option value="tab">Internal tab format</option>\r\n+ <option value="tab_noheaders">Internal tab format without headers</option>\r\n+ <option value="fasta">FASTA format</option>\r\n+ <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>\r\n+ <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>\r\n+ <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>\r\n+ <option value="fastq">FASTQ format</option>\r\n+ <option value="phylip">Phylip format</option>\r\n+ <option value="relaxed_phylip">relaxed Phylip format</option>\r\n+ <option value="nexus">NEXUS format</option>\r\n+ <option value="nexml">DnaCharacterMatrix in NeXML format</option>\r\n+ <option value="genbank">Genbank flat file format</option>\r\n+ </param>\r\n+ <when value="tab">\r\n+ <param name="extension1" type="hidden" value="tab"/>\r\n+ </when>\r\n+ <when value="phylip">\r\n+ <param name="extension1" type="hidden" value="phy"/>\r\n+ </when>\r\n+ <when value="fasta">\r\n+ <param name="extension1" type="hidden" value="fas"/>\r\n+ </when>\r\n+ <when value="fasta_hapview">\r\n+ <param name="extension1" type="hidden" value="fas"/>\r\n+ </when>\r\n+ <when value="fasta_gbexport">\r\n+ <param name="extension1" type="hidden" value="fas"/>\r\n+ </when>\r\n+ <when value="mold_fasta">\r\n+ <param name="extension1" type="hidden" value="fas"/>\r\n+ </when>\r\n+ <when value="fastq">\r\n+ <param name="extension1" type="hidden" value="fq"/>\r\n+ </when>\r\n+ <when value="tab_noheaders">\r\n+ <param name="extension1" type="hidden" value="tab"/>\r\n+ </when>\r\n+ <when value="relaxed_phylip">\r\n+ <param name="extension1" type="hidden" value="phy"/>\r\n+ </when>\r\n+ '..b'="tabular">\r\n+ <change_format>\r\n+ <when input="outformat_and_extension.outformat1" value="phylip" format="phylip" />\r\n+ <when input="outformat_and_extension.outformat1" value="fasta" format="fasta" />\r\n+ <when input="outformat_and_extension.outformat1" value="tab_noheaders" format="tabular" />\r\n+ <when input="outformat_and_extension.outformat1" value="tab" format="tabular" />\r\n+ <when input="outformat_and_extension.outformat1" value="fasta_hapview" format="fasta" />\r\n+ <when input="outformat_and_extension.outformat1" value="fastq" format="fastq" />\r\n+ <when input="outformat_and_extension.outformat1" value="relaxed_phylip" format="phylip" />\r\n+ <when input="outformat_and_extension.outformat1" value="nexus" format="nexus" />\r\n+ <when input="outformat_and_extension.outformat1" value="nexml" format="nexml" />\r\n+ <when input="outformat_and_extension.outformat1" value="genbank" format="gb" />\r\n+ <when input="outformat_and_extension.outformat1" value="mold_fasta" format="fasta" />\r\n+ </change_format>\r\n+ </data>\r\n+ </outputs>\r\n+ <tests>\r\n+ <test>\r\n+ <param name="input1" value="DNAconvert_examplefile2_iTaxoTools_0_1.fas"/>\r\n+ <param name="informat1" value="fasta" />\r\n+ <param name="outformat1" value="tab" />\r\n+ <output name="output1" file="DNAtestout_1.tab"/>\r\n+ </test>\r\n+ <test>\r\n+ <param name="input1" value="DNAconvert_examplefile3_iTaxoTools_0_1.tab"/>\r\n+ <param name="informat1" value="tab" />\r\n+ <param name="outformat1" value="phylip" />\r\n+ <output name="output1" file="DNAtestout_2.phy"/>\r\n+ </test>\r\n+ </tests> \r\n+ <help><![CDATA[\r\n+\r\n+**DNAconvert**\r\n+\r\n+A program to convert between different file formats containing DNA sequences. \r\n+Written by V. Kharchev in the framework of the iTaxoTools project.\r\n+Galaxy wrapper for DNAconvert 0.1 written in 2022/2023 by F. Fischell.\r\n+\r\n+Standalone executables with graphical user interface of the newest version of ASAP for Windows and Mac are available from:\r\n+\r\n+http://itaxotools.org/\r\n+\r\n+https://github.com/iTaxoTools/iTaxoTools-Executables/releases\r\n+\r\n+\r\n+For more information, see the iTaxoTools manual available at:\r\n+http://itaxotools.org/\r\n+\r\n+**Usage**\r\n+\r\n+- Specify an input file and the input file format, as well as the desired output file format. \r\n+- DNAconvert will "sanitize" sequence names by replacing special characters by underscores\r\n+- For formats that require unique sequence names, DNAconvert can automatically rename sequnces by adding consecutive numbers to the names\r\n+- An important feature of DNAconvert is the option to use tab-delimited files which allows curating sequence data sets with metadata in spreadsheet editors. Refer to the iTaxoTool manual for details.\r\n+\r\n+**Supported formats**\r\n+\r\n+* `tab` = tsv: [Internal tab format][1] = tab-delimited text\r\n+\r\n+* `tab_noheaders`: [Internal tab format][1] without headers = tab-delimited text without headers\r\n+\r\n+* `fasta`: FASTA format\r\n+\r\n+* `phylip`: Phylip format\r\n+\r\n+* `relaxed_phylip`: relaxed Phylip format (with no restriction on the length of sequence names)\r\n+\r\n+* `fasta_hapview`: FASTA format with sequence names formatted for Haplotype Viewer\r\n+\r\n+* `fastq`: FASTQ format\r\n+\r\n+* `fasta_gbexport`: FASTA format with sequence names adjusted for export into GenBank repository\r\n+\r\n+* `nexus`: NEXUS format\r\n+\r\n+* `nexml`: DnaCharacterMatrix in NeXML format\r\n+\r\n+* `genbank`: Genbank flat file format\r\n+\r\n+* `mold_fasta`: FASTA format with sequence name matching requirements for the tool MolD *\r\n+\r\n+\r\n+**Recognised extension**\r\n+\r\n+Automatic recognition of file format based on extension in file name not yet available in the Galaxy implementation. \r\n+\r\n+\r\n+\r\n+\r\n+\r\n+ ]]></help>\r\n+ <citations>\r\n+\t<citation type="doi">\r\n+\t 10.11646/megataxa.6.2.1 \r\n+\t</citation>\r\n+ </citations>\r\n+</tool>\r\n' |
| b |
| diff -r 000000000000 -r aef9a0c2c65e README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sun Jan 29 16:32:28 2023 +0000 |
| [ |
| @@ -0,0 +1,107 @@ +# DNAconvert +Convert between different file formats containing genetic information. + +## Installation +Install the latest version directly using pip (requires Python 3.8 or later): +``` +pip install git+https://github.com/iTaxoTools/DNAconvert.git#egg=DNAconvert +``` + +## Executables +Download and run the standalone executables without installing Python.</br> +[See the latest release here.](https://github.com/iTaxoTools/DNAconvert/releases/latest) + +## Usage + usage: DNAconvert [-h] [--cmd] [--allow_empty_sequences] + [--informat INFORMAT] [--outformat OUTFORMAT] + [infile] [outfile] + DNAconvert + + positional arguments: + infile the input file + outfile the output file + + optional arguments: + -h, --help show this help message and exit + --cmd activates the command-line interface + --allow_empty_sequences + set this to keep the empty sequences in the output + file + --disable_automatic_renaming + disables automatic renaming, may result in duplicate + sequence names in Phylip and Nexus files + --informat INFORMAT format of the input file + --outformat OUTFORMAT + format of the output file + +### Batch processing + +If `infile` is a directory, all files in it will be converted. In this case `informat` and `outformat` arguments are required. + +Specifying names of the output files: +* `outfile` contains a '#' character: '#' will be replaced with the base names of input files. +* `outfile` is a directory: the output files will be written in it, with the same names as input files. + +## Supported formats +* `tab`: [Internal tab format][1] +* `tab_noheaders`: [Internal tab format][1] without headers +* `fasta`: FASTA format +* `relaxed_phylip`: relaxed Phylip format +* `fasta_hapview`: FASTA format for Haplotype Viewer +* `phylip`: Phylip format +* `fastq`: FASTQ format +* `fasta_gbexport`: FASTA format for export into Genbank repository +* `nexus`: NEXUS format +* `nexml`: DnaCharacterMatrix in NeXML format +* `genbank`: Genbank flat file format +* `mold_fasta`: FASTA format with sequence name matching requirements for the tool MolD + +## Recognised extension +If format is not provided, the program can infer it from the file extension + +Currently recognised: +* `.tab`, `.txt`, `.tsv`: [Internal tab format][1] +* `.fas`, `.fasta`, `.fna`: FASTA format +* `.rel.phy`: relaxed Phylip format +* `.hapv.fas`: FASTA format for Haplotype Viewer +* `.phy`: Phylip format +* `.fastq`, `.fq`: FASTQ format +* `.fastq.gz`, `.fq.gz`: FASTQ format compressed with Gzip +* `.gb.fas`: FASTA format for export into Genbank repository +* `.nex`: NEXUS format +* `.xml`: NeXML format +* `.gb`: Genbank flat file format + +Files with extension `.gz` are uncompressed automatically + +## Adding new formats +[Link to documentation](docs/ADDING_FORMATS.md) + +[1]: docs/TAB_FORMAT.md + +## Options +DNAconvert uses two parsers for NEXUS format: internal (default) and the one from python-nexus package. + +In the file `DNAconvert/config.json` (found in `%APPDATA%\iTaxoTools` or in `$XDG_CONFIG_HOME$/`) the key-value pair +``` +"nexus_parser" : "(method)"" +``` +determines the parser. `(method)` is either `internal` or `python-nexus`. + +## Generating an executable +Using [PyInstaller](http://www.pyinstaller.org) is recommended. You should first clone the repository and install DNAconvert with all dependencies (includes PyInstaller): +``` +git clone https://github.com/iTaxoTools/DNAconvert.git +cd DNAconvert +pip install ".[dev]" +``` + +After the following instruction, the directory `dist` will be created (among others) and the executable will be inside it: +``` +pyinstaller scripts/DNAconvert.spec +``` + +## Dependencies +Automatically installed when using pip: +* [python\-nexus](https://pypi.org/project/python-nexus/) +* [dendropy](https://pypi.org/project/DendroPy/) |
| b |
| diff -r 000000000000 -r aef9a0c2c65e test-data/DNAconvert_examplefile2_iTaxoTools_0_1.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DNAconvert_examplefile2_iTaxoTools_0_1.fas Sun Jan 29 16:32:28 2023 +0000 |
| b |
| b'@@ -0,0 +1,71 @@\n+>Paradoxophyla_palmata_Ranomafana_FGMV_2002_466\r\n+TAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTTATTAAATTCCAATTTTAACACAAAGCCCTTCATCATTACTGAATGAT\r\n+>Paradoxophyla_palmata_Ranomafana_FGMV_2002_467\r\n+CGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTT\r\n+>Paradoxophyla_palmata_Andasibe_FGMV_2002_2371\r\n+CGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATTTACCTCACCACTTTTTGCCTACCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTTTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCATAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATCAAAACATCCCGCTTACACCGTGACCATATCTGTGAGACCCAGATCATTTTGAGCTAAAAACCTAGCCTAATTTTTTATACATACAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGTAATAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATCCAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGCGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTGACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGAATACAACCTAAGACACTGGGTAATGAATTAAATTAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAGATAGCGTTAAAGCTTCATCACTCCTTTA\r\n+>Paradoxophyla_palmata_Ranomafana_FGMV_2002_634\r\n+CGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCT'..b'GTCTATGAACCCATAGTAGCAACACCTCAAGAAAACCCTACTACAATATACGTTAACCTTACACCAGAACATTGCCGGAAAGATTAAAAAAAGAGGAAGGAACTCGGCAAATTTTAACCCCGCCTGTTTACCAAAAACATCGCCTCCTGACATAACTATAGGAGGTCCAGCCTGCCCAGTGACAAAGTTAAACGGCCGCGGTACCCTAACCGTGCGAAGGTAGCGCAATCACTTGTTCTTTAAATGAGGACTAGTATGAATGGCATCACGAGGGTTATACTGTCTCCCTCTTTCAATCAGTGAAACTGATCTTCCCGTGAAGAAGCGGGAATATACCTATAAGACGAGAAGACCCCATGGAGCTTAAAACTCAGTATCAACTGCCCTACTTACAAACCCTATTAACCAAGCAGATATGACTACTAGTTTTCGGTTGGGGTGACCGCGGAGCAAAATAAAACCTCCACGATGAAAGGAACTAACCTCCTAATCCAAGAGCTACTACTCTAAGAATCAACAAATTGACATTTATTGATCCAATTTTTTTGATCAACGAACCAAGTTACCCTGGGGATAACAGCGCAATCCATTTCAAGAGCCCCTATCGAC\r\n+>Scaphiophryne_brevis_Anakao_ZCMV_12842\r\n+CGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAAATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATTTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTAA\r\n+>Scaphiophryne_brevis_Anakao_ZCMV_12843\r\n+CGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAGATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATCTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTA\r\n+>Scaphiophryne_calcarata_B_Menabe_ZCMV_4701\r\n+TAATCGATTATCCCCGATAAACCTCACCATTTCT-------------AGCCAA-TCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCTAATTAGTGAGCTTAAAGATC-CCTCCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGTGGGAAGCAATGGGCTACAATTTCTAACTTAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAGAGAAAATAGAGAGTTCTCTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGC-CCATAAACGTTTTCTAACACCTAACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACCTAAAGCATCTCGCTTACACCGAGAACATGTTTGTTCAACCCAGATCATTTTGAGCCAAAAACCTAGCCCAA--CTAATGCAAATGCCTCAACAAACC-TAACCACAAC---AAATAAAACA-TTTTTATCTTCTAGTAAAGGCGATTGAAAAATAATTAAGGAGCTATAGAGACAGTACCGCAAGGGAAA-GGTGAAATAAAAATGAAATAACTTTAAAGCAAAAT-TAAGCAGAGACACAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCAAACCAAGCAAAATGCATTTATAGTTTGACACCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTC-AAGGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAGCCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTACCTTAAGTTTTATTGTACTACCAAATACACCCCTAAACTTAAGAGCTATTCAAATAAGGTACAGCCTATTTGAAACAGGAGACAACCTAAAACACAGGGTAATGACACTCT-TTAAGTGACCAAGTGGGCCTAAAAGCAGCCAACTTTCAAACAGCGTTAAAGCTTCGTCACTCCATCTGATTAATACCTAAACCCATACAAAACCCTTTACC\r\n+\r\n' |
| b |
| diff -r 000000000000 -r aef9a0c2c65e test-data/DNAconvert_examplefile3_iTaxoTools_0_1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DNAconvert_examplefile3_iTaxoTools_0_1.tab Sun Jan 29 16:32:28 2023 +0000 |
| b |
| b'@@ -0,0 +1,38 @@\n+seqid\tOrganism\tCountry\tVoucher number\tsequence\r\n+specimen1\t Paradoxophyla palmata\tRanomafana\tFGMV 2002.466\tTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTTATTAAATTCCAATTTTAACACAAAGCCCTTCATCATTACTGAATGAT\r\n+specimen2\tParadoxophyla palmata\tRanomafana\tFGMV 2002.467\tCGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTT\r\n+specimen3\tParadoxophyla palmata\tAndasibe\tFGMV 2002.2371\tCGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATTTACCTCACCACTTTTTGCCTACCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTTTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCATAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATCAAAACATCCCGCTTACACCGTGACCATATCTGTGAGACCCAGATCATTTTGAGCTAAAAACCTAGCCTAATTTTTTATACATACAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGTAATAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATCCAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGCGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTGACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGAATACAACCTAAGACACTGGGTAATGAATTAAATTAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAGATAGCGTTAAAGCTTCATCACTCCTTTA\r\n+specimen4\tParadoxophyla palmata\tRanomafana\tFGMV 2002.634\tCGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAAC'..b'CACCTCAAGAAAACCCTACTACAATATACGTTAACCTTACACCAGAACATTGCCGGAAAGATTAAAAAAAGAGGAAGGAACTCGGCAAATTTTAACCCCGCCTGTTTACCAAAAACATCGCCTCCTGACATAACTATAGGAGGTCCAGCCTGCCCAGTGACAAAGTTAAACGGCCGCGGTACCCTAACCGTGCGAAGGTAGCGCAATCACTTGTTCTTTAAATGAGGACTAGTATGAATGGCATCACGAGGGTTATACTGTCTCCCTCTTTCAATCAGTGAAACTGATCTTCCCGTGAAGAAGCGGGAATATACCTATAAGACGAGAAGACCCCATGGAGCTTAAAACTCAGTATCAACTGCCCTACTTACAAACCCTATTAACCAAGCAGATATGACTACTAGTTTTCGGTTGGGGTGACCGCGGAGCAAAATAAAACCTCCACGATGAAAGGAACTAACCTCCTAATCCAAGAGCTACTACTCTAAGAATCAACAAATTGACATTTATTGATCCAATTTTTTTGATCAACGAACCAAGTTACCCTGGGGATAACAGCGCAATCCATTTCAAGAGCCCCTATCGAC\r\n+specimen35\tScaphiophryne brevis\tAnakao\tZCMV 12842\tCGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAAATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATTTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTAA\r\n+specimen36\tScaphiophryne brevis\tAnakao\tZCMV 12843\tCGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAGATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATCTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTA\r\n+specimen37\tScaphiophryne calcarata B\tMenabe \tZCMV 4701\tTAATCGATTATCCCCGATAAACCTCACCATTTCT-------------AGCCAA-TCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCTAATTAGTGAGCTTAAAGATC-CCTCCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGTGGGAAGCAATGGGCTACAATTTCTAACTTAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAGAGAAAATAGAGAGTTCTCTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGC-CCATAAACGTTTTCTAACACCTAACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACCTAAAGCATCTCGCTTACACCGAGAACATGTTTGTTCAACCCAGATCATTTTGAGCCAAAAACCTAGCCCAA--CTAATGCAAATGCCTCAACAAACC-TAACCACAAC---AAATAAAACA-TTTTTATCTTCTAGTAAAGGCGATTGAAAAATAATTAAGGAGCTATAGAGACAGTACCGCAAGGGAAA-GGTGAAATAAAAATGAAATAACTTTAAAGCAAAAT-TAAGCAGAGACACAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCAAACCAAGCAAAATGCATTTATAGTTTGACACCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTC-AAGGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAGCCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTACCTTAAGTTTTATTGTACTACCAAATACACCCCTAAACTTAAGAGCTATTCAAATAAGGTACAGCCTATTTGAAACAGGAGACAACCTAAAACACAGGGTAATGACACTCT-TTAAGTGACCAAGTGGGCCTAAAAGCAGCCAACTTTCAAACAGCGTTAAAGCTTCGTCACTCCATCTGATTAATACCTAAACCCATACAAAACCCTTTACC\r\n' |
| b |
| diff -r 000000000000 -r aef9a0c2c65e test-data/DNAtestout_1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DNAtestout_1.tab Sun Jan 29 16:32:28 2023 +0000 |
| b |
| b'@@ -0,0 +1,36 @@\n+seqid\tsequence\n+Paradoxophyla_palmata_Ranomafana_FGMV_2002_466\tTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTTATTAAATTCCAATTTTAACACAAAGCCCTTCATCATTACTGAATGAT\n+Paradoxophyla_palmata_Ranomafana_FGMV_2002_467\tCGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTT\n+Paradoxophyla_palmata_Andasibe_FGMV_2002_2371\tCGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATTTACCTCACCACTTTTTGCCTACCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTTTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCATAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATCAAAACATCCCGCTTACACCGTGACCATATCTGTGAGACCCAGATCATTTTGAGCTAAAAACCTAGCCTAATTTTTTATACATACAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGTAATAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATCCAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGCGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTGACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGAATACAACCTAAGACACTGGGTAATGAATTAAATTAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAGATAGCGTTAAAGCTTCATCACTCCTTTA\n+Paradoxophyla_palmata_Ranomafana_FGMV_2002_634\tCGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACC'..b'CTCACTGGCACTTATCGTCTATGAACCCATAGTAGCAACACCTCAAGAAAACCCTACTACAATATACGTTAACCTTACACCAGAACATTGCCGGAAAGATTAAAAAAAGAGGAAGGAACTCGGCAAATTTTAACCCCGCCTGTTTACCAAAAACATCGCCTCCTGACATAACTATAGGAGGTCCAGCCTGCCCAGTGACAAAGTTAAACGGCCGCGGTACCCTAACCGTGCGAAGGTAGCGCAATCACTTGTTCTTTAAATGAGGACTAGTATGAATGGCATCACGAGGGTTATACTGTCTCCCTCTTTCAATCAGTGAAACTGATCTTCCCGTGAAGAAGCGGGAATATACCTATAAGACGAGAAGACCCCATGGAGCTTAAAACTCAGTATCAACTGCCCTACTTACAAACCCTATTAACCAAGCAGATATGACTACTAGTTTTCGGTTGGGGTGACCGCGGAGCAAAATAAAACCTCCACGATGAAAGGAACTAACCTCCTAATCCAAGAGCTACTACTCTAAGAATCAACAAATTGACATTTATTGATCCAATTTTTTTGATCAACGAACCAAGTTACCCTGGGGATAACAGCGCAATCCATTTCAAGAGCCCCTATCGAC\n+Scaphiophryne_brevis_Anakao_ZCMV_12842\tCGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAAATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATTTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTAA\n+Scaphiophryne_brevis_Anakao_ZCMV_12843\tCGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAGATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATCTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTA\n+Scaphiophryne_calcarata_B_Menabe_ZCMV_4701\tTAATCGATTATCCCCGATAAACCTCACCATTTCT-------------AGCCAA-TCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCTAATTAGTGAGCTTAAAGATC-CCTCCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGTGGGAAGCAATGGGCTACAATTTCTAACTTAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAGAGAAAATAGAGAGTTCTCTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGC-CCATAAACGTTTTCTAACACCTAACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACCTAAAGCATCTCGCTTACACCGAGAACATGTTTGTTCAACCCAGATCATTTTGAGCCAAAAACCTAGCCCAA--CTAATGCAAATGCCTCAACAAACC-TAACCACAAC---AAATAAAACA-TTTTTATCTTCTAGTAAAGGCGATTGAAAAATAATTAAGGAGCTATAGAGACAGTACCGCAAGGGAAA-GGTGAAATAAAAATGAAATAACTTTAAAGCAAAAT-TAAGCAGAGACACAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCAAACCAAGCAAAATGCATTTATAGTTTGACACCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTC-AAGGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAGCCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTACCTTAAGTTTTATTGTACTACCAAATACACCCCTAAACTTAAGAGCTATTCAAATAAGGTACAGCCTATTTGAAACAGGAGACAACCTAAAACACAGGGTAATGACACTCT-TTAAGTGACCAAGTGGGCCTAAAAGCAGCCAACTTTCAAACAGCGTTAAAGCTTCGTCACTCCATCTGATTAATACCTAAACCCATACAAAACCCTTTACC\n' |
| b |
| diff -r 000000000000 -r aef9a0c2c65e test-data/DNAtestout_2.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DNAtestout_2.phy Sun Jan 29 16:32:28 2023 +0000 |
| b |
| b'@@ -0,0 +1,36 @@\n+35 1082\n+Paradoxo_0 TAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTTATTAAATTCCAATTTTAACACAAAGCCCTTCATCATTACTGAATGAT\n+Paradoxo_1 CGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATTTAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGTGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTAACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTAAGACACAGGGTAATGAATTAAATAAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAAAAGCGTTAAAGCTTCATCACTCCTTTT\n+Paradoxo_2 CGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATTTACCTCACCACTTTTTGCCTACCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTTTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCATAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATCAAAACATCCCGCTTACACCGTGACCATATCTGTGAGACCCAGATCATTTTGAGCTAAAAACCTAGCCTAATTTTTTATACATACAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGTAATAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAGCAAAACAAAGTAGAGATCCAACCTCGTACCTTTTGCATCATGATCTAGCAAGTCCGCCCAAGCAAAAAGCATTTAAGTTTGACTTCCCGAAACTAAACGAGCTACTTCAAAACAGCCTTCCCAGGGCCAACTCATCTCTGTTGCAAAAGAGTGAGAAGATTTTCAAGTAGCGGTGATAAACCTACCGAGCTTAGAGATAGCTGGTTATTCAGGAAAAAGATTTTAGTCTGACCTTAAGTTTTTCTTACATCTCAATATTTTCTTAAACTTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGAATACAACCTAAGACACTGGGTAATGAATTAAATTAGTGACTAAGTGGGCCTAAAAGCAGCCAACTTAAAGATAGCGTTAAAGCTTCATCACTCCTTTA\n+Paradoxo_3 CGAGCTCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCCCCCCGATTTACCTCACCACTTTTTGCCTATCCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGACTCTTAGTGAGCCATAAGATTATTACATCAACACGTCAGGTCAAGGTGCAGCCCACAAAGTGGAAAGAAATGGGCTACAATTTCTAACCTAGAACACACGAAAGACTACATGAAACACAGCCATGAAGGTGGATTTAGTAGTAAAAAGAAAATAGAGCGTTCTTTTTAACCAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGCCAACAAAAGTTTTTAACACAACTAAGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAATTAAAACATCCCGCTTACACCGTGACCATATCTGTGAAACTCAGATCATTTTGAGCTGAAAACCTAGCCTAACTTTTATATACATTCAACCTATCTACATCTCAACTTTAACTAAAACATTCTTTCATATTAGTAAAGGCGATTGAAAATTTCTAAGAGCCATAGCAACAGTACCGCAAGGGAAAAGTGAAATAAAAATGAAATAAATCTAAAG'..b'CTCCATAATTATATGGAGAACACTATGCTAGAACTAGTAACAAGAAGAAGACCTTCTCCAAAATGTAAGTGTAAGCCAAAATGAACACCTCACTGGCACTTATCGTCTATGAACCCATAGTAGCAACACCTCAAGAAAACCCTACTACAATATACGTTAACCTTACACCAGAACATTGCCGGAAAGATTAAAAAAAGAGGAAGGAACTCGGCAAATTTTAACCCCGCCTGTTTACCAAAAACATCGCCTCCTGACATAACTATAGGAGGTCCAGCCTGCCCAGTGACAAAGTTAAACGGCCGCGGTACCCTAACCGTGCGAAGGTAGCGCAATCACTTGTTCTTTAAATGAGGACTAGTATGAATGGCATCACGAGGGTTATACTGTCTCCCTCTTTCAATCAGTGAAACTGATCTTCCCGTGAAGAAGCGGGAATATACCTATAAGACGAGAAGACCCCATGGAGCTTAAAACTCAGTATCAACTGCCCTACTTACAAACCCTATTAACCAAGCAGATATGACTACTAGTTTTCGGTTGGGGTGACCGCGGAGCAAAATAAAACCTCCACGATGAAAGGAACTAACCTCCTAATCCAAGAGCTACTACTCTAAGAATCAACAAATTGACATTTATTGATCCAATTTTTTTGATCAACGAACCAAGTTACCCTGGGGATAACAGCGCAATCCATTTCAAGAGCCCCTATCGAC\n+Scaphio_32 CGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAAATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATTTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTAA\n+Scaphio_33 CGAGCCCAAGCTTAAAACCCAAAGGACTTGACGGTGTCCCACCCACCTAGAGGAGCCTGTTCTATAATCGATTCTCCCCGATAAACCTCACCGCTTCTAGCCTATCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCCAATTAGTGAGCTTAAAGATCTTTTTCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGCGGGAAGCAATGGGCTACAATTTCTAAAATAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAAAGAAAATAGAGAGTTCTTTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAATGCCCATAAATGTTAACTAACACCCCACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACTTAAAGCATCCCGCTTACACCGAGAACATGTCTGTTAAATCCAGATCATTTTGAGCTAAAAACCTAGCTCAATTTATGCAAATGCCTAAACCAACCCTCCCGAGATCAAACAAAACATTTAATTTTTTAGTAAAGGCGATTGAAAGAATACTAGAAGCTATAATAATAGTACCGCAAGGGAAAGGTGAAATAAAAATGAAATAACTTTAAAGCAAAATAAAGCAGAGATTTAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCCAACCAAGCAAAACGCACTTACAGTTTGACCCCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTTCAAGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAACCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTGCCTTAAGCTTACCCTTATTCCAAAATATTCCCATAAGCCTAAGAGCCATTCAAATAAGGTACAGCCTATTTGAAACAGGATACAACCTCCAACACAGGGTAATGATATCTTCAAATGTGACTAAGTGGGCCTAAAAGCAGCCAACTTTTAAATAGCGTTAAAGCTTCATCACTTA\n+Scaphio_34 TAATCGATTATCCCCGATAAACCTCACCATTTCT-------------AGCCAA-TCAGCCTGTATACCTCCGTCGTAAGCTTACCATATGAACGCTAATTAGTGAGCTTAAAGATC-CCTCCATCAACACGTCAGGTCAAGGTGCAGCTCACGAAGTGGGAAGCAATGGGCTACAATTTCTAACTTAGAACACACGAAAGACTACATGAAACACAGTCATGAAGGCGGATTTAGCAGTAAAGAGAAAATAGAGAGTTCTCTTTAATTAGGCGCTGGGACGCGTACACACCGCCCGTCACCCTCTTCAAACGC-CCATAAACGTTTTCTAACACCTAACCGCACAATAGAAGAGGTAAGTCGTAACACGGTAAGCGTACTGGAAAGTGCGCTTGGACTAACAAAATGTAGCTTAACCTAAAGCATCTCGCTTACACCGAGAACATGTTTGTTCAACCCAGATCATTTTGAGCCAAAAACCTAGCCCAA--CTAATGCAAATGCCTCAACAAACC-TAACCACAAC---AAATAAAACA-TTTTTATCTTCTAGTAAAGGCGATTGAAAAATAATTAAGGAGCTATAGAGACAGTACCGCAAGGGAAA-GGTGAAATAAAAATGAAATAACTTTAAAGCAAAAT-TAAGCAGAGACACAACCTCGTACCTTTTGCATCATGGTCTAGCTAGTCAAACCAAGCAAAATGCATTTATAGTTTGACACCCCGAAACTAGGTGAGCTACTTCAAAACAGCCTC-AAGGGGCCAACCCGTCTCTGTTGCAAAAGAGTGGGAAGATTTTCAAGTAGAGGTGACAGACCTACCGAGCCTAGAGATAGCTGGTTATTCAGGAAAAGGATTTAAGTCCTACCTTAAGTTTTATTGTACTACCAAATACACCCCTAAACTTAAGAGCTATTCAAATAAGGTACAGCCTATTTGAAACAGGAGACAACCTAAAACACAGGGTAATGACACTCT-TTAAGTGACCAAGTGGGCCTAAAAGCAGCCAACTTTCAAACAGCGTTAAAGCTTCGTCACTCCATCTGATTAATACCTAAACCCATACAAAACCCTTTACC\n' |