| Previous changeset 1:6362669c440a (2015-10-02) Next changeset 3:df98a0425c8d (2015-12-11) |
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Commit message:
planemo upload |
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added:
fastme.xml test-data/newick test-data/newick.log test-data/phylip tool_dependencies.xml |
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removed:
fastMe_main/fastme.xml fastMe_main/test-data/newick fastMe_main/test-data/newick.log fastMe_main/test-data/phylip fastMe_main/tool_dependencies.xml |
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| diff -r 6362669c440a -r 40200a22dba3 fastMe_main/fastme.xml --- a/fastMe_main/fastme.xml Fri Oct 02 10:55:52 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,255 +0,0 @@ -<tool id="sniplay_fastme" name="FastME" version="1.1.0"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Calculate distance tree for an alignment file</description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - <requirement type="package" version="2.1.4">fastme - </requirement> - </requirements> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - - <!-- [REQUIRED] The command to execute --> - <command> - fastme --input_data=$input_data --dna=$model --output_tree=$fileout - #if str( $distance ) == "SPR": - --spr - #elif str( $distance )[:3] == "NNI" : - #if str( $distance ) == "NNI_B" : - --nni=B - #else : - --nni=O - #end if - - #else : - --method=$distance - #end if - > $fileout_log - </command> - - - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" /> - <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" /> - <param name="fileout_label2" type="text" value="Unused" label="none" help="Output name for files" /> - <param name="model" type="select" label="Evolutionary model" > - <option value="p">p-distance</option> - <option value="Y">RY symetric</option> - <option value="R">RY</option> - <option value="J">JC69</option> - <option value="K">K2P</option> - <option value="1">F81</option> - <option value="4" selected="true">F84</option> - <option value="T">TN93</option> - <option value="L">LogDet</option> - </param> - <param name="distance" type="select" label="Distance methode" > - <option value="B">TaxAdd_BalME</option> - <option value="O">TaxAdd_OLSME</option> - <option value="I" selected="true">BIONJ</option> - <option value="N">NJ</option> - <option value="U">UNJ</option> - <option value="NNI_B">NNI_BalME</option> - <option value="NNI_O">NNI_OLS</option> - <option value="SPR">SPR</option> - </param> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> - <data name="fileout" type="data" format="txt" label="${fileout_label}" /> - </outputs> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - - <test> - <param name="filein" value="phylip" /> - <param name="model" value="4"/> - <param name="distance" value="I"/> - <output name="fileout" file="newick" /> - <output name="fileout_log" file="newick.log" /> - </test> - - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - -.. class:: infomark - -**Authors** - - | Richard Desper and Olivier Gascuel, - | Journal of Computational Biology 19(5), 687-705, 2002. - | Molecular Biology and Evolution 21(3), 587-598, 2004. - | Please cite these papers if you use this software in your publications. - - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr - ---------------------------------------------------- - - -====== -FastMe -====== - ------------ -Description ------------ - - - FastME - A distance based phylogeny reconstruction algorithm. - - FastME showed better topological accuracy than NJ, - BIONJ, WEIGHBOR and FITCH, in all evolutionary - conditions we tested, which include large range - deviations from molecular clock and substitution rates. - - - ------------------ -Workflow position ------------------ - -**Upstream tools** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -Readseq phylip conversion phylip -=========== ========================== ======= - - -**Downstream tools** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -Rooting out tree Newick -=========== ========================== ======= - - ----------- -Input file ----------- - -Phylip file - Phylip file with sequence alignments - - ----------- -Parameters ----------- - -Output name - Output base name for the ouput files - -Evolutionary model - Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet. - -Distance methode - FastME computes a tree using a distance algorithm. You may choose this method/topologie from: TaxAdd_BalME, TaxAdd_OLSME, BIONJ (default), NJ, UNJ, NNI_BalME, NNI_OLS or SPR - ------------- -Output files ------------- - -Output_name - Resulting tree at Newick format - -Output_name.log - Log file - ------------- -Dependencies ------------- -FastME - http://www.atgc-montpellier.fr/fastme - - - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -Philip file ------------ - -:: - - 168 5125 - IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT - KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT - -Parameters -========== - -Output name -> Newick tree - -Evolutionary model -> F84 - -Distance methode -> BIONJ - -Output files -============ - -Newick tree ------------ - -:: - - (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... - - - </help> - - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex"> -@article{Lefort30062015, -author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier}, -title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program}, -year = {2015}, -doi = {10.1093/molbev/msv150}, -abstract ={FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).}, -URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract}, -eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html}, -journal = {Molecular Biology and Evolution} -} - - </citation> - - </citations> - - -</tool> |
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| diff -r 6362669c440a -r 40200a22dba3 fastMe_main/test-data/newick --- a/fastMe_main/test-data/newick Fri Oct 02 10:55:52 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863); - |
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| diff -r 6362669c440a -r 40200a22dba3 fastMe_main/test-data/newick.log --- a/fastMe_main/test-data/newick.log Fri Oct 02 10:55:52 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ - - . This analysis will run on 2 threads. - -# Analysing dataset 1 - - . Computing pairwise distances... - - . Computing tree... - - . Time used 0h00m05s |
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| diff -r 6362669c440a -r 40200a22dba3 fastMe_main/test-data/phylip --- a/fastMe_main/test-data/phylip Fri Oct 02 10:55:52 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,17579 +0,0 @@\n- 168 5125\n-IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT\n-DOURADOPRE AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-KINANDANGP GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n-CAAWA/FORT GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-VARYLAVA90 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n-CIRAD358 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAAATCAAAT\n-PCT4_SA_4_ GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n-YUNLU7 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-BAKUNGH GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-BAGANANASA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-NHTA10 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATAATAAAG TAATACTAAT\n-MALAGKITPI GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n-IR65907-20 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-KAKANI2 GAGAAAGAAT TCAGTTGTTC TCAACCATTA AGATATTTGA ATAAAAAGAT\n-DOURADOAGU AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-IRAT13 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-DAWASANRED GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTACTAAAG TAATACTAAT\n-CHUAN4 GCGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTACGAAAG TAATACTAAT\n-MOROBEREKA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-IRAT362 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-PULULAPA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n-MAHAE GAGAACCGTC CTGTAAGTAC TCTTGCTTTA GGAACGAAAG TAATACTAAT\n-WAB56-50 AAGATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-ORYZICASAB AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n-MARAVILHA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-IDSA77 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n-INDANE GAGAACCGTC CTGTAAGTAC TCTTGTTATA AGAACTAAAG TAATACTAAT\n-DINORADO GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-RT1031-69 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-IR63380-16 GAAATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-VARYSOMOTR GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-HAWMOM GAGAACCGTC CTGTAAGTAC TCTTGCTTAA AATACGAAAG TAATACTAAT\n-IRAT364 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-TREMBESE GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATTAAG TAATACTAAT\n-NIPPONBARE GAAAACCGTC CTGTAACCTT GATTGTTATA AGAACTAAAG TATTACTAAT\n-AZUCENA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n-BABER GAGAACCGTC CTGTAACCTT GATTGTTATA AGAAATAAAG TAATACTAAT\n-WAB56-125 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-BENGALYVAK GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAAAT\n-KETANMENAH GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTAATAAAG TATATCTAAT\n-BULUPANDAK GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n-ARIAS GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTAATAAAG TATATCTAAT\n-GOMPA2 GAGAAAGAAT TCAGTTGTTC TCAACCATTA AGATATTTGA ATTAAAAAAT\n-IRAT335 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-M202 GAGAACCGTC CTGTAACCTT GATTGTTATA GGTAATAAAG TAATACTAAT\n-IR53236-27 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-IR65907-18 GAGATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-P5589-1-1- AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-MANDRIRAVI AAGAACCGTC CTGTAAGTAC TCTTGCTTAA AGTAATAAAG TAATACTAAT\n-PALAWAN GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAACTAAAG TATATCAACA\n-CNA-7_BO_1 GAGTACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAAAAAAGAT\n-IRAT257 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-TANDUI GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n-KETANLUMBU GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n-IRAT109 GAGAACCGTC CTGTAACCTT GATTGTTATA AGAACTAAAG TAATACTAAT\n-PCT11_0_0_ AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n-KANIRANGA GAGAACCGTC CTGTAAGTAC'..b'\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTACAGTACG GTGCGCCTGA AAGAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- AAATACTGTG GTCTATTAAA TTGTA\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- ATTCAGTACT GACTGCCTGA ATGTT\n- TTACAGTACG GTGCGCCTGA AAGAT\n- AAACGGTACT ATCTGCTAAA TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- AAATACTGTG GTCTATTAAA TTGTA\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- AAATACTGTG GTCTATTAAA TTGTA\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTACAGTACG GTGCGCCTGA AAGAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- ATTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- AAATACTGTG GTCTATTAAA TTGTA\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTACAGTACG GTGCGCCTGA AAGAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- ATTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGTGTG GTCTATTAAA TTGTA\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGTGTG GTCTATTAAA TTGTA\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- ATTCGGAACT AACTGCTTAT TTATT\n- TTACAGTACG GTGCGCCTGA AAGAT\n- TTACAGTACG GTGCGCCTGA AAGAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n- TTTCGGAACT AACTGCTTAT TTAAT\n- TTTCGGAACT AACTGCTTAT TTATT\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n-\n' |
| b |
| diff -r 6362669c440a -r 40200a22dba3 fastMe_main/tool_dependencies.xml --- a/fastMe_main/tool_dependencies.xml Fri Oct 02 10:55:52 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="fastme" version="2.1.4"> - <repository changeset_revision="fbf2a5cac7e3" name="package_fastme_2_1_4" owner="gandres" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r 6362669c440a -r 40200a22dba3 fastme.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastme.xml Fri Dec 11 09:16:34 2015 -0500 |
| [ |
| @@ -0,0 +1,252 @@ +<tool id="sniplay_fastme" name="Fassqa" version="1.1.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Calculate distance tree for an alignment file</description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + <requirement type="package" version="2.1.4">fastme</requirement> + </requirements> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + + <!-- [REQUIRED] The command to execute --> + <command> + fastme --input_data=$input_data --dna=$model --output_tree=$fileout + #if str( $distance ) == "SPR": + --spr + #elif str( $distance )[:3] == "NNI" : + #if str( $distance ) == "NNI_B" : + --nni=B + #else : + --nni=O + #end if + + #else : + --method=$distance + #end if + > $fileout_log + </command> + + + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="input_data" type="data" format="txt" optional="false" label="Phylip input" /> + <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" /> + <param name="model" type="select" label="Evolutionary model" > + <option value="p">p-distance</option> + <option value="Y">RY symetric</option> + <option value="R">RY</option> + <option value="J">JC69</option> + <option value="K">K2P</option> + <option value="1">F81</option> + <option value="4" selected="true">F84</option> + <option value="T">TN93</option> + <option value="L">LogDet</option> + </param> + <param name="distance" type="select" label="Distance methode" > + <option value="B">TaxAdd_BalME</option> + <option value="O">TaxAdd_OLSME</option> + <option value="I" selected="true">BIONJ</option> + <option value="N">NJ</option> + <option value="U">UNJ</option> + <option value="NNI_B">NNI_BalME</option> + <option value="NNI_O">NNI_OLS</option> + <option value="SPR">SPR</option> + </param> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> + <data name="fileout" type="data" format="txt" label="${fileout_label}" /> + </outputs> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + + <test> + <param name="input_data" value="phylip" /> + <param name="model" value="4"/> + <param name="distance" value="I"/> + <output name="fileout" file="newick" /> + </test> + + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + +.. class:: infomark + +**Authors** + + | Richard Desper and Olivier Gascuel, + | Journal of Computational Biology 19(5), 687-705, 2002. + | Molecular Biology and Evolution 21(3), 587-598, 2004. + | Please cite these papers if you use this software in your publications. + + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + + +====== +FastMe +====== + +----------- +Description +----------- + + + FastME - A distance based phylogeny reconstruction algorithm. + + FastME showed better topological accuracy than NJ, + BIONJ, WEIGHBOR and FITCH, in all evolutionary + conditions we tested, which include large range + deviations from molecular clock and substitution rates. + + + +----------------- +Workflow position +----------------- + +**Upstream tools** + +=========== ========================== ======= +Name output file(s) format +=========== ========================== ======= +Readseq phylip conversion phylip +=========== ========================== ======= + + +**Downstream tools** + +=========== ========================== ======= +Name output file(s) format +=========== ========================== ======= +Rooting out tree Newick +=========== ========================== ======= + + +---------- +Input file +---------- + +Phylip file + Phylip file with sequence alignments + + +---------- +Parameters +---------- + +Output name + Output base name for the ouput files + +Evolutionary model + Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet. + +Distance methode + FastME computes a tree using a distance algorithm. You may choose this method/topologie from: TaxAdd_BalME, TaxAdd_OLSME, BIONJ (default), NJ, UNJ, NNI_BalME, NNI_OLS or SPR + +------------ +Output files +------------ + +Output_name + Resulting tree at Newick format + +Output_name.log + Log file + +------------ +Dependencies +------------ +FastME + http://www.atgc-montpellier.fr/fastme + + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Philip file +----------- + +:: + + 168 5125 + IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT + KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT + +Parameters +========== + +Output name -> Newick tree + +Evolutionary model -> F84 + +Distance methode -> BIONJ + +Output files +============ + +Newick tree +----------- + +:: + + (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... + + + </help> + + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex"> +@article{Lefort30062015, +author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier}, +title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program}, +year = {2015}, +doi = {10.1093/molbev/msv150}, +abstract ={FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).}, +URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract}, +eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html}, +journal = {Molecular Biology and Evolution} +} + + </citation> + + </citations> + + +</tool> |
| b |
| diff -r 6362669c440a -r 40200a22dba3 test-data/newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newick Fri Dec 11 09:16:34 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863); + |
| b |
| diff -r 6362669c440a -r 40200a22dba3 test-data/newick.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/newick.log Fri Dec 11 09:16:34 2015 -0500 |
| b |
| @@ -0,0 +1,10 @@ + + . This analysis will run on 2 threads. + +# Analysing dataset 1 + + . Computing pairwise distances... + + . Computing tree... + + . Time used 0h00m05s |
| b |
| diff -r 6362669c440a -r 40200a22dba3 test-data/phylip --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phylip Fri Dec 11 09:16:34 2015 -0500 |
| b |
| b'@@ -0,0 +1,17579 @@\n+ 168 5125\n+IRAT112 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KARASUKARA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT\n+DOURADOPRE AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KINANDANGP GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+CAAWA/FORT GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+VARYLAVA90 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+CIRAD358 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAAATCAAAT\n+PCT4_SA_4_ GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+YUNLU7 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+BAKUNGH GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+BAGANANASA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+NHTA10 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATAATAAAG TAATACTAAT\n+MALAGKITPI GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n+IR65907-20 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KAKANI2 GAGAAAGAAT TCAGTTGTTC TCAACCATTA AGATATTTGA ATAAAAAGAT\n+DOURADOAGU AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IRAT13 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+DAWASANRED GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTACTAAAG TAATACTAAT\n+CHUAN4 GCGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTACGAAAG TAATACTAAT\n+MOROBEREKA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IRAT362 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+PULULAPA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n+MAHAE GAGAACCGTC CTGTAAGTAC TCTTGCTTTA GGAACGAAAG TAATACTAAT\n+WAB56-50 AAGATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+ORYZICASAB AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+MARAVILHA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IDSA77 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTACA\n+INDANE GAGAACCGTC CTGTAAGTAC TCTTGTTATA AGAACTAAAG TAATACTAAT\n+DINORADO GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+RT1031-69 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IR63380-16 GAAATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+VARYSOMOTR GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+HAWMOM GAGAACCGTC CTGTAAGTAC TCTTGCTTAA AATACGAAAG TAATACTAAT\n+IRAT364 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+TREMBESE GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATTAAG TAATACTAAT\n+NIPPONBARE GAAAACCGTC CTGTAACCTT GATTGTTATA AGAACTAAAG TATTACTAAT\n+AZUCENA GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n+BABER GAGAACCGTC CTGTAACCTT GATTGTTATA AGAAATAAAG TAATACTAAT\n+WAB56-125 AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+BENGALYVAK GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAAAT\n+KETANMENAH GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTAATAAAG TATATCTAAT\n+BULUPANDAK GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n+ARIAS GAGAACCGTC CTGTAAGTAC TCTTGTTATA GGTAATAAAG TATATCTAAT\n+GOMPA2 GAGAAAGAAT TCAGTTGTTC TCAACCATTA AGATATTTGA ATTAAAAAAT\n+IRAT335 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+M202 GAGAACCGTC CTGTAACCTT GATTGTTATA GGTAATAAAG TAATACTAAT\n+IR53236-27 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+IR65907-18 GAGATCCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+P5589-1-1- AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+MANDRIRAVI AAGAACCGTC CTGTAAGTAC TCTTGCTTAA AGTAATAAAG TAATACTAAT\n+PALAWAN GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAACTAAAG TATATCAACA\n+CNA-7_BO_1 GAGTACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAAAAAAGAT\n+IRAT257 GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+TANDUI GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TATATCAACA\n+KETANLUMBU GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGAAATAAAG TATATCAAAT\n+IRAT109 GAGAACCGTC CTGTAACCTT GATTGTTATA AGAACTAAAG TAATACTAAT\n+PCT11_0_0_ AAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT\n+KANIRANGA GAGAACCGTC CTGTAAGTAC'..b'\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ ATTCAGTACT GACTGCCTGA ATGTT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ AAACGGTACT ATCTGCTAAA TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ ATTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ AAATACTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ ATTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGTGTG GTCTATTAAA TTGTA\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ ATTCGGAACT AACTGCTTAT TTATT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTACAGTACG GTGCGCCTGA AAGAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+ TTTCGGAACT AACTGCTTAT TTAAT\n+ TTTCGGAACT AACTGCTTAT TTATT\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n' |
| b |
| diff -r 6362669c440a -r 40200a22dba3 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Dec 11 09:16:34 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fastme" version="2.1.4"> + <repository changeset_revision="fbf2a5cac7e3" name="package_fastme_2_1_4" owner="gandres" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |