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nylander / beast2phy

Convert output trees from BEAST to other formats
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BEAST2 to MrBayes Expecting ';' Instead found ':' #1

Open Alexei-Kassian opened 1 year ago

Alexei-Kassian commented 1 year ago

Dear Johan, I have a BEAST2 output file with sampled trees. I want to analyze it with MrBayes to obtain a majority rule consensus tree. I converted the BEAST file:

beast2phy.pl --format=mb --outfile=test.t test.trees

This is an example. Original BEAST syntax:

_tree STATE_0 = ((((1[&rate=0.007351478177251801]:0.6821029877791007,2[&rate=0.006735905750528852]:0.8413029524934701)[&rate=0.011346987157382039]:2.0582335418469304,(((((5[&rate=0.00593980788317566]:0.0,(6[&rate=0.002876118478952018]:0.0,(7[&rate=0.0071551987121419875]:0.0,(((8[&rate=0.0017350561596703325]:0.7724472467677833,(11[&rate=0.003559374671199588]:0.6423165039212633,(13[&rate=0.007457414081971797]:0.4056865177837033,14[&rate=0.004707084454842623]:0.3403283181302862)[&rate=0.0029933098274789165]:0.23662998613755998)[&rate=0.002876118478952018]:0.13013074284652004)[&rate=0.00379625365921241]:0.15990691392123135,10[&rate=0.001462631513176089]:0.9323541606890147)[&rate=0.003255173256902891]:0.019927545524258905,(9[&rate=0.0031840734153133488]:0.7403609156622648,12[&rate=0.0043818765740708835]:0.7403609156622648)[&rate=0.0034334939283033336]:0.21192079055100876)[&rate=0.007457414081971797]:0.9506770050392852)[&rate=0.0017350561596703325]:0.47101638637794774)[&rate=0.0033577795467098115]:0.9940987719688512)[&rate=0.005748178019419008]:1.7120425284481184,((18[&rate=0.0043818765740708835]:0.1993358690188479,19[&rate=0.004182923546646661]:0.1993358690188479)[&rate=0.0037261689017361404]:0.7980984775672605,20[&rate=0.006590367144388293]:0.9974343465861084)[&rate=0.006661788709088827]:4.082682051461368)[&rate=0.0039621059887193135]:0.32412586184014636,(15[&rate=0.004358833599187632]:0.03807623162573148,(16[&rate=0.0028889580665307866]:0.2714071304313083,17[&rate=0.005890117138125287]:0.2714071304313083)[&rate=0.0018757135190608136]:1.3487821312157455)[&rate=0.0062091246308745955]:3.7840529982405684)[&rate=0.009272503707208868]:0.40997934878422093,(((101[&rate=0.0020221887617111974]:0.5114874141666488,(((((102[&rate=0.005491780972318927]:0.1300866838632332,103[&rate=0.0014941058778438763]:0.9363340576524398)[&rate=0.003255173256902891]:0.13873774902974867,104[&rate=9.069006928696829E-4]:1.0750718066821885)[&rate=0.008247602117419848]:0.050934026794299925,108[&rate=0.00245923307649412]:0.47204353517716846)[&rate=0.004876447711034487]:0.030902012622809893,((((105[&rate=0.0024711031548388935]:0.0227007961922134,106[&rate=0.0032986881804451056]:0.0227007961922134)[&rate=0.003850223611841267]:0.28860489729253164,110[&rate=0.002712742302335519]:0.311305693484745)[&rate=0.00245923307649412]:0.29504439181179376,109[&rate=0.0021883495594936376]:0.6063500852965388)[&rate=0.001539745389934493]:0.3037064869477112,107[&rate=0.0034029510483741614]:0.91005657224425)[&rate=0.002762363538790261]:0.24685127385504835)[&rate=0.0039621059887193135]:0.7441348179056926,((111[&rate=0.0029800981669338687]:0.35403099533956817,(112[&rate=0.0018507007328846194]:0.22207029962078662,((113[&rate=0.0020221887617111974]:0.21367736490917755,((((114[&rate=8.003432674093666E-4]:0.18881455810531855,116[&rate=0.0040398849560830145]:0.18881455810531855)[&rate=0.0023176526259386107]:0.19235292940240556,115[&rate=0.005375089098208432]:0.3811674875077241)[&rate=0.0026758577145501498]:0.3216861832786273,((118[&rate=8.587074229386931E-4]:0.5140028180103909,121[&rate=0.004525691323533426]:0.5140028180103909)[&rate=0.0019128619654665367]:0.0449382938286389,119[&rate=0.0019981229528998564]:0.5589411118390298)[&rate=0.0039621059887193135]:0.14391255894732158)[&rate=0.004734353179222841]:0.15384057794527284,117[&rate=0.005452113193623758]:0.09371335146214377)[&rate=0.002247153253803673]:0.09098771649788762)[&rate=0.0027004172540268023]:0.029774330334357058,120[&rate=0.0016951009636647987]:0.3775081998761348)[&rate=8.003432674093666E-4]:0.42074715806159346)[&rate=0.0034799826520696534]:0.14477920276321243)[&rate=0.003418178601806663]:0.10339259585947347,(122[&rate=0.00222364595061649]:0.035825835973520403,123[&rate=0.0049667428438992765]:1.0335897269508485)[&rate=0.002058093625713289]:0.6127855252972998)[&rate=0.00222364595061649]:0.2546674117568426)[&rate=0.004936193637774623]:0.2367791538030244)[&rate=0.007063906165547193]:2.132860012405247,((148[&rate=0.006893086991623584]:0.5116957194505432,((149[&rate=0.002435534587545611]:0.22965419312683033,(150[&rate=0.0018507007328846194]:0.16615128950507874,151[&rate=0.0014301843775338195]:0.9726407207550158)[&rate=0.001379370262243453]:0.29032291915770037)[&rate=0.009022764086903634]:0.1411986287304403,(((152[&rate=0.006390491201804096]:0.18240930787466925,153[&rate=0.003527320703161725]:0.3846308597540493)[&rate=0.005532262378635763]:0.24127181463160574,(155[&rate=0.001267420223727322]:0.34046044200987924,(156[&rate=0.0026149491225408643]:0.6341772316869528,157[&rate=0.0016679764774446047]:0.6341772316869528)[&rate=0.002578707756756661]:0.17204712438854475)[&rate=0.005375089098208432]:0.16838500975084292)[&rate=0.0037089655872437426]:0.3047206931070706,154[&rate=0.0026514134799934014]:0.23276567945904003)[&rate=0.002518741771179387]:0.1248322097097454)[&rate=0.005375089098208432]:1.054342216198087)[&rate=0.0026514134799934014]:0.31279927196756985,(158[&rate=0.002712742302335519]:0.428106285098766,((159[&rate=0.002627078054740023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After conversion to the MrBayes format:

tree rep.0 = ((((1:0.682102987779101,2:0.841302952493470):2.058233541846930,(((((5:0.000000000000000,(6:0.000000000000000,(7:0.000000000000000,(((8:0.772447246767783,(11:0.642316503921263,(13:0.405686517783703,14:0.340328318130286):0.236629986137560):0.130130742846520):0.159906913921231,10:0.932354160689015):0.019927545524259,(9:0.740360915662265,12:0.740360915662265):0.211920790551009):0.950677005039285):0.471016386377948):0.994098771968851):1.712042528448118,((18:0.199335869018848,19:0.199335869018848):0.798098477567260,20:0.997434346586108):4.082682051461368):0.324125861840146,(15:0.038076231625731,(16:0.271407130431308,17:0.271407130431308):1.348782131215746):3.784052998240568):0.409979348784221,(((101:0.511487414166649,(((((102:0.130086683863233,103:0.936334057652440):0.138737749029749,104:1.075071806682188):0.050934026794300,108:0.472043535177168):0.030902012622810,((((105:0.022700796192213,106:0.022700796192213):0.288604897292532,110:0.311305693484745):0.295044391811794,109:0.606350085296539):0.303706486947711,107:0.910056572244250):0.246851273855048):0.744134817905693,((111:0.354030995339568,(112:0.222070299620787,((113:0.213677364909178,((((114:0.188814558105319,116:0.188814558105319):0.192352929402406,115:0.381167487507724):0.321686183278627,((118:0.514002818010391,121:0.514002818010391):0.044938293828639,119:0.558941111839030):0.143912558947322):0.153840577945273,117:0.093713351462144):0.090987716497888):0.029774330334357,120:0.377508199876135):0.420747158061593):0.144779202763212):0.103392595859473,(122:0.035825835973520,123:1.033589726950848):0.612785525297300):0.254667411756843):0.236779153803024):2.132860012405247,((148:0.511695719450543,((149:0.229654193126830,(150:0.166151289505079,151:0.972640720755016):0.290322919157700):0.141198628730440,(((152:0.182409307874669,153:0.384630859754049):0.241271814631606,(155:0.340460442009879,(156:0.634177231686953,157:0.634177231686953):0.172047124388545):0.168385009750843):0.304720693107071,154:0.232765679459040):0.124832209709745):1.054342216198087):0.312799271967570,(158:0.428106285098766,((159:0.741682493094589,160:0.532661946697015):0.399672782457574,161:1.141355275552162):0.538997244888245):1.090951236368406):1.499378073404449):0.873051610964593,((124:0.278713851466177,((125:0.717483055210944,126:0.717483055210944):0.874925870592902,(((127:0.681056661904254,((128:0.589092588338606,((129:0.323031898387278,132:0.323031898387278):0.113921779820373,130:0.436953678207651):0.152138910130955):0.045109457273065,131:0.634202045611671):0.181686322327342):0.473421000771185,((135:0.439587981478277,(((136:0.224783948017349,139:0.224783948017349):0.366992034070219,137:0.591775982087568):0.366280072953961,138:0.242764440736732):0.106114256978990):0.137964595919648,((140:0.131517561835042,141:0.889443593525716):0.261418312297940,((142:0.117125094001792,143:0.862635497173479):0.175736288576963,(144:0.105184133269619,145:0.105184133269619):0.933187652480823):0.112490120073215):0.051273002116511):0.087174460770031):0.059434742626479,(133:0.766211100863207,134:0.766211100863207):0.582533010473470):0.243664814467169):0.803890833753465):0.872797337556963,(146:0.242981062300197,147:0.368397386817906):0.790615209859618):1.874636344063581):0.670488167493988):0.266353393928867,((((74:0.323252728778199,75:0.323252728778199):0.996470698224467,76:1.319723427002666):1.183536973092977,77:2.069871812711312):0.434127553372888,(((78:0.193379294396107,(84:0.098549170920291,(85:0.157257584573372,86:0.157257584573372):0.224705250052997):0.745691628349770):0.208346381728909,((79:0.605538110448653,(80:0.574635188212468,(81:0.099939997120886,82:0.099939997120886):0.474695191091582):0.030902922236185):0.373202282965828,83:0.978740393414481):0.357260451290567):0.039821871356089,(((((87:0.126284558527185,(88:0.420189266375957,89:0.420189266375957):0.258038599304070):0.210812346733403,(90:0.412913563818162,(94:0.317731328625058,95:0.317731328625058):0.393435654057928):0.177873229730444):0.106642587024515,((91:0.208742115747802,93:0.208742115747802):0.611203106876329,92:0.146113228352590):0.175737576813815):0.095805466051897,((97:0.302673233453290,(98:0.111239010067706,99:0.111239010067706):0.191434223385584):0.587325187098467,100:0.889998420551757):0.201489844938086):0.102834014033197,96:0.570611840587061):0.181500436538098):1.561565237407393):3.143187049132180):0.068102622694742):0.140080624067886,((21:0.282288690568395,(22:1.066929677267116,((23:2.460410902958106,((((24:0.565260175550743,25:0.565260175550743):0.673491380051072,(((26:0.462749145201599,27:0.462749145201599):0.128953240606101,(28:0.495389451795476,((29:0.159348721822261,30:0.159348721822261):0.161593850113449,32:0.320942571935709):0.174446879859767):0.096312934012224):0.517676653044598,31:1.109379038852299):0.129372516749516):0.391030922966222,33:1.629782478568037):0.577451881111165,34:2.207234359679202):0.253176543278904):0.671957129921537,((((35:0.700541702774475,36:0.700541702774475):0.246880411212065,37:0.947422113986540):1.145553193096826,(38:1.646930630023372,39:1.646930630023372):0.446044677059993):0.349682787264757,(((40:0.113276639062052,(41:0.052897169033898,42:0.052897169033898):0.060379470028154):0.583844781648945,(43:0.502058031703012,44:0.502058031703012):0.195063389007985):0.858594236497499,45:1.555715657208496):0.886942437139626):0.689709938531522):0.360908386485264):0.450293458837266):1.036787955831612,(46:0.574594917535756,(((((47:1.585251366697582,(50:2.212790052765937,(51:1.778748503410462,52:1.778748503410462):0.434041549355475):0.086641149976283):0.104053147365492,(48:0.667329726545467,53:1.830037017035720):0.573447333071991):0.431923925974704,49:1.179617713737304):0.080819390011827,(72:0.155707349476368,73:0.155707349476368):2.760520316617875):0.167509037112017,(54:1.541808363053778,((55:0.515555045532513,(57:0.761983724477177,((((((58:0.670272173392985,(63:0.531865642504609,64:0.531865642504609):0.138406530888376):0.030824920297670,61:0.701097093690654):0.237453765895602,((59:0.530047219264320,60:0.530047219264320):0.194204890510259,62:0.724252109774579):0.214298749811678):0.154706305060430,(66:1.093114961221029,(((68:0.303763839148298,71:0.303763839148298):0.233397769450795,70:0.537161608599093):0.162638350170757,69:0.699799958769850):0.393315002451179):0.000142203425658):0.324344830671904,65:1.417601995318591):0.241469845388936,67:1.659071840707527):0.644588740256856):0.284045630813403):0.213923446118465,56:0.316767816110699):0.164146218147785):0.117960827162223):0.915008728393724):0.981612402433803):1.308400415329551):0.395978299636983,(3:0.350301967637851,4:0.271474616635198):4.953831592999250):0.000000000000000;

MrBayes however returns an error when importing test.t:

Found one tree block in file "test.t" with 37004 trees in last block

Tree reading status:

  0      10      20      30      40      50      60      70      80      90     100
  v-------v-------v-------v-------v-------v-------v-------v-------v-------v-------v
  *      Expecting ';'

Instead found ':' in command 'Tree' Error in command "Tree" The error occurred when reading char. 6632 on line 180 in the file 'test.nex' Error in command "Execute"

P.S. MrBayes proper *.t files are analyzed without problems.

Alexei-Kassian commented 1 year ago

I found the problem. At the very end of each tree in the obtained MrBayes' *.t file, the sequence ):0.000000000000000; should be changed to ); After that MyBayes can read it.