Repository 'fastme'
hg clone https://toolshed.g2.bx.psu.edu/repos/dereeper/fastme

Changeset 0:e119d00db28c (2018-04-16)
Commit message:
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
added:
fastme.xml
test-data/TreeTn93BionjSpr.nwk
test-data/newick
test-data/newick.log
test-data/phylip
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diff -r 000000000000 -r e119d00db28c fastme.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastme.xml Mon Apr 16 09:00:15 2018 -0400
[
b'@@ -0,0 +1,361 @@\n+<tool id="fastme" name="FastME" version="2.0.0">\n+    <description>Distance-based inference of phylogenetic trees</description>\n+    <requirements>\n+        <requirement type="package" version="2.1.5">fastme</requirement>\n+    </requirements>\n+    <stdio>\n+        <exit_code range="1:" level="fatal" />\n+    </stdio>\n+    <version_command>\n+        <![CDATA[ fastme --version ]]>\n+    </version_command>\n+    <command>fastme -f 6\n+                    --input_data=$input\n+                    --output_tree=$outputTree\n+                    --output_matrix=$outputMatrix\n+                    --output_info=$outputLog\n+                    --nb_threads=\\${GALAXY_SLOTS:-1}\n+\n+                    #if $typeChoice.datatype =="d"\n+                        --dna=$typeChoice.modeldna\n+\n+                    #else if $typeChoice.datatype =="p"\n+                        --protein=$typeChoice.modelprot\n+\n+                    #else if $typeChoice.datatype =="cfg":\n+                         ## Read information of sequence type\n+                         ## read an info file to choose which option set and set a model by default\n+                         #set $info = open( str($input_info) ).read()\n+                         #if \'dna\' in $info:\n+                                --dna=T\n+                         #else if \'protein\' in $info:\n+                               --protein=L\n+                         #end if\n+                    #end if\n+\n+                    #if $gammaChoice.gamma == "true"\n+                        --gamma=$gammaChoice.rate\n+                    #end if\n+\n+                    $distance\n+                    $equilibrium\n+                    $removeGap\n+                    $treeRefinement\n+\n+                    #if $bootChoice.boot == "true"\n+                        --output_boot=$outputBoostrap\n+                        --bootstrap=$bootChoice.replicates\n+                    #end if\n+\n+                    >> tmp_stdout;\n+                    cat tmp_stdout > $outputLog;\n+\n+    </command>\n+    <inputs>\n+        <param name="input" type="data" format="phylip, phy" label="Fastme input" help="Phylip Alignment or Matrix file"/>\n+        <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />\n+        <conditional name="typeChoice">\n+            <param name="datatype" type="select" display="radio" label="Data type" >\n+                <option value="d">DNA</option>\n+                <option value="p">Protein</option>\n+                <option value="m">Matrix</option>\n+                <option value="cfg">Config file</option>\n+            </param>\n+            <when value="d">\n+                <param name="modeldna" type="select" label="Evolutionary model">\n+                    <option value="4">F84</option>\n+                    <option value="R">RY</option>\n+                    <option value="1">F81</option>\n+                    <option value="J">JC69</option>\n+                    <option value="K">K2P</option>\n+                    <option value="T" selected="true">TN93</option>\n+                    <option value="p">p-distance</option>\n+                </param>\n+            </when>\n+            <when value="p">\n+                <param name="modelprot" type="select" label="Evolutionary model">\n+                    <option value="L">LG</option>\n+                    <option value="W">WAG</option>\n+                    <option value="J">JTT</option>\n+                    <option value="h">Day off</option>\n+                    <option value="C">CpRev</option>\n+                    <option value="D">DCMut</option>\n+                    <option value="b">HIVb</option>\n+                    <option value="I">HIVw</option>\n+                    <option value="M">MtREV</option>\n+                    <option value="R">RtREV</option>\n+                    <option value="p">p-distance</option>\n+                </param>\n+            </when>\n+            <when value="m"/>\n+            <when '..b'file.\n+\n+  -B output_bootstrap_trees_file, --output_boot=output_bootstrap_trees_file\n+        Use this option if you want FastME to write bootstrap trees\n+        in the bootstrap trees file.\n+\n+  -a, --append\n+        Use this option to append results to existing output files (if any).\n+        By default output files will be overwritten.\n+\n+  -m method, --method=method\n+        FastME computes a tree using a distance algorithm.\n+        You may choose this method from:\n+        TaxAdd_(B)alME, TaxAdd_(O)LSME, B(I)ONJ (default),\n+        (N)J or (U)NJ.\n+\n+  -d model, --dna=model\n+        Use this option if your input data file contains DNA sequences alignment(s).\n+        You may also indicate the evolutionary [model] which can be choosen from:\n+        (p)-distance, R(Y) symmetric, (R)Y, (J)C69, (K)2P, F8(1), F8(4) (default), (T)N93, (L)ogDet.\n+\n+  -p model, --protein=model\n+        Use this option if your input data file contains protein sequences alignment(s).\n+        You may also indicate the evolutionary [model] which can be choosen from:\n+        (p)-distance, (F)81 like, (L)G (default), (W)AG, (J)TT, Day(h)off, (D)CMut, (C)pRev,\n+        (M)tREV, (R)tREV, HIV(b), H(I)Vw or FL(U).\n+\n+  -r, --remove_gap\n+        Use this option to completely remove any site which has a gap in\n+        any sequence. By default, FastME is doing pairwise deletion of gaps.\n+\n+  -e, --equilibrium\n+        The equilibrium frequencies for DNA are always estimated by counting\n+        the occurence of the nucleotides in the input alignment.\n+        For amino-acid sequences, the equilibrium frequencies are estimated\n+        using the frequencies defined by the substitution model.\n+        Use this option if you whish to estimate the amino-acid frequencies\n+        by counting their occurence in the input alignment.\n+\n+  -g alpha, --gamma=alpha\n+       Use this option if you wish to have gamma distributed rates across sites.\n+       By default, FastME runs with no gamma variation.\n+       If running FastME with gamma distributed rates across sites, the [alpha] default value is 1.0.\n+       Only helpful when the input data file contains sequences alignment(s).\n+\n+  -n NNI, --nni=NNI\n+        Use this option to do [NNI] tree topology improvement.\n+        You may choose the [NNI] type from:\n+        NNI_(B)alME (default) or NNI_(O)LS.\n+\n+  -s, --spr\n+        Use this option to do SPR tree topology improvement.\n+\n+  -w branch, --branch_length=branch\n+        Use this option to indicate the branch length to assign to the tree.\n+        Only helpful when not improving the tree topology (no NNI nor SPR).\n+        You may choose the branch length from:\n+        (B)alLS (default), (O)LS or (n)one. (n)one is only available with BIONJ, NJ or UNJ.\n+\n+  -D datasets, --datasets=datasets\n+        Use this option to indicate the number of datasets in your input\n+        data file. Default value is 1.\n+\n+  -b replicates, --bootstrap=replicates\n+        Use this option to indicate the number of replicates FastME will\n+        do for bootstrapping. Default value is 0.\n+        Only helpful when the input data file contains sequences alignment(s).\n+\n+  -z seed, --seed=seed\n+        Use this option to initialize randomization with seed value. Only helpful when bootstrapping.\n+\n+  -c  Use this option if you want FastME only to compute distance matrix.\n+        Only helpful when the input data file contains sequences alignment(s).\n+\n+  -T number_of_threads, --nb_threads=number_of_threads\n+        Use this option to set the number of threads to use.\n+        Default number of threads is 4.\n+\n+  -v value, --verbose=value\n+        Sets the verbose level to value [0-3]. Default value is 0\n+\n+  -V, --version\n+        Prints the FastME version.\n+\n+  -h, --help  Display this usage.\n+\n+\n+    ]]></help>\n+    <citations>\n+       <citation type="doi">10.1093/molbev/msv150</citation>\n+       <citation type="doi">10.1089/106652702761034136</citation>\n+    </citations>\n+</tool>\n'
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diff -r 000000000000 -r e119d00db28c test-data/TreeTn93BionjSpr.nwk
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TreeTn93BionjSpr.nwk Mon Apr 16 09:00:15 2018 -0400
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+(((((((LUDAN:0.058984,(CUBA65:0.034439,(IR53236-27:0.041957,AZUCENA:0.012204):0.029488):0.020093):0.008005,DAVAO:0.048408):0.011654,((((((((IR60080-46:0.073381,IR71525-19:0.081382):0.061527,(((IR66421-10:0.134294,IR66421-09:0.121164):0.041337,CNA-7_BO_1:0.134453):0.051254,IR68704-14:0.163754):0.021776):0.065639,IR71524-44:0.028063):0.021365,IR47686-09:0.057759):0.022300,((((PACHOLINHA:0.041859,CANELADEFE:0.059086):0.004361,((((((((((MANANELATR:0.038768,(GRAZI:0.021717,ARROZCEBAD:0.029974):0.004941):0.005843,KOMOJAMANI:0.053807):0.010143,(MAINTIMOLO:0.053033,((TSIPALA89:0.006858,VARYLAVADE:0.031063):0.027904,MITSANGANA:0.088914):0.092122):0.011560):0.006339,(((GANIGI:0.036593,PULULAPA:0.048674):0.021103,GOGO:0.069129):0.006323,(((POENOETHIT:0.049142,KETANLUMBU:0.033967):0.022674,((REKETMAUN:0.069587,((CICIHBETON:0.020594,(GUNDILKUNI:0.024824,BULUPANDAK:0.015495):0.009148):0.027065,PADIBOENAR:0.054889):0.009380):0.005181,MOLOK:0.051715):0.012343):0.018121,PADIKASALL:0.100786):0.108445):0.021157):0.004985,MANDRIRAVI:0.050277):0.006028,(((((((((YANCAOUSSA:0.005056,MOROBEREKA:0.005651):0.005266,PATEBLANCM:0.005159):0.017444,VARYMALADY:0.018874):0.009484,((((GOGOLEMPUK:0.001829,GOGOLEMPAK:0.001505):0.037625,TREMBESE:0.007331):0.066736,((JIMBRUKJOL:0.043940,KETANKONIR:0.041578):0.011282,KANIRANGA:0.040609):0.017465):0.012315,(VARYMADINI:0.027247,BENGALYVAK:0.048956):0.009924):0.015059):0.009376,(FOHISOMOTR:0.004605,VARYSOMOTR:0.008121):0.032972):0.011575,(IRAT366:0.048828,WAB706-3-4:0.045445):0.012808):0.003293,IRAT364:0.049189):0.002694,IRAT104:0.058606):0.006775,RT1031-69:0.046709):0.005400):0.008137,IRAT234:0.038810):0.001863,(((((((INDANE:0.099717,(((DAM:0.045319,CHAPHUMA:0.085867):0.010324,((NHTA10:0.072750,(((JAOHAW:0.051853,KHAODAM:0.028241):0.009103,(MAHAE:0.038718,(KHAOKAPXAN:0.006210,HAWMOM:0.009164):0.037485):0.021070):0.008644,KU115:0.049535):0.001157):0.006831,((((VIETNAM3:0.037472,SENG:0.036113):0.014694,((NABESHI:0.012036,KARASUKARA:0.009092):0.026831,(PEHPINUO:0.074467,(CHUAN3:0.023026,CHUAN4:0.023256):0.018349):0.008358):0.017309):0.013977,VIETNAM1:0.041553):0.017970,((((((JUMALI:0.084283,LAMBAYQUE1:0.214891):0.062918,KAKANI2:0.046870):0.012237,GOMPA2:0.056630):0.142704,JUMULA2:0.056316):0.108686,(NEPHOAVANG:0.112158,(((NPE826:0.018102,NPE253:0.019379):0.027020,(NIPPONBARE:0.021473,(GIZA171:0.009077,M202:0.072279):0.025584):0.026150):0.015272,BABER:0.213505):0.005930):0.013092):0.061233,(((GEMJYAJYAN:0.011812,YANGKUMRED:0.015400):0.011575,DANGREY:0.022664):0.019775,DAWASANRED:0.033667):0.056680):0.033975):0.009554):0.004348):0.004108,CHALOYOE:0.078446):0.002877):0.010299,NHTA5:0.174102):0.014171,YUNLU7:0.085770):0.018809,CIRAD358:0.109908):0.016155,CUIABANA:0.064911):0.030163,CAIAPO:0.068242):0.022987,((CIRAD488:0.078455,((KUROKA:0.110911,IRAT144:0.031562):0.039313,(IRAT212:0.027762,PRIMAVERA:0.080508):0.010963):0.041983):0.031608,((CIRAD392:0.019225,IRAT380:0.032899):0.023331,CIRAD394:0.068753):0.032089):0.030517):0.004235):0.007114,(63-104:0.031158,((((((PCT11_0_0_:0.087249,P5589-1-1-:0.044844):0.043028,ESPERANZA:0.089017):0.019333,(((CIRAD403:0.039495,(CIRAD409:0.044435,MARAVILHA:0.088411):0.036497):0.029782,(CURINCA:0.098481,(ref:1.799674,PCT4_SA_4_:0.093913):0.135987):0.087392):0.031499,((((IRAT216:0.010172,((COLOMBIA1:0.159197,((IR63372-08:-0.004292,IR65907-18:0.064421):0.076143,IR65907-20:0.026896):0.010825):0.003895,IR47684-05:0.009618):0.007150):0.021875,(WAB56-50:0.025508,WAB56-125:0.055841):0.021942):0.032087,IDSA77:0.027876):0.030596,((IR65261-19:0.110151,IR63380-16:0.057031):0.050131,ORYZICASAB:0.035980):0.018196):0.013137):0.019039):0.024807,(CT13582-15:0.101068,IRAT362:0.031224):0.014934):0.017206,((ARAGUAIA:0.097889,(IRAT335:0.095237,IRAT112:0.018559):0.006657):0.011455,IRAT257:0.044438):0.014206):0.006090,((IRAT2:0.006150,(((62667:0.001694,IRAT109:0.099502):0.002007,IRAT177:0.002973):0.002454,IRAT13:0.004418):0.002047):0.008318,IRAT170:0.015591):0.016552):0.013701):0.010608):0.008742,(((EARLYMUTAN:0.015291,(IAC25:0.005550,(DOURADOAGU:0.001923,DOURADOPRE:0.001412):0.012771):0.003721):0.014573,BICOBRANCO:0.031417):0.005801,((((IAC47:0.008672,(IAC165:0.000877,VARYLAVA90:0.001277):0.004708):0.003948,HD1-4:0.015766):0.006482,GUARANI:0.014371):0.003849,IGUAPECATE:0.038047):0.006343):0.004463):0.009071):0.004980,TRESMESES:0.026050):0.002407,(OS4:0.026433,OS6:0.011283):0.021989):0.007745):0.002950,(CANAROXA:0.016223,KINANDANGP:0.052864):0.019815):0.010435,CAAWA/FORT:0.059481):0.006273,MALAGKITPI:0.065879):0.005210):0.003293,BINULAWAN:0.063713):0.007478,(DINORADO:0.073753,(BAGANANASA:0.045282,BAKUNGH:0.059768):0.027823):0.001457):0.004023,(SPEAKER:0.068748,((KEDAYAN:0.080968,(TANDUI:0.083000,KETANMENAH:0.095067):0.018450):0.002215,(ARIAS:0.064870,RATHAL:0.093722):0.028878):0.018054):0.011765):0.027188,PALAWAN:0.025533,KENDINGA5H:0.039037);
+
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diff -r 000000000000 -r e119d00db28c test-data/newick
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/newick Mon Apr 16 09:00:15 2018 -0400
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 000000000000 -r e119d00db28c test-data/newick.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/newick.log Mon Apr 16 09:00:15 2018 -0400
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 000000000000 -r e119d00db28c test-data/phylip
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phylip Mon Apr 16 09:00:15 2018 -0400
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'