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Copy pathaaRS_XrayCrystalStructuresOnly.xml
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aaRS_XrayCrystalStructuresOnly.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" version="2.0">
<data id="AARS" name="alignment">
<userDataType spec='beast.evolution.datatype.TwentyState' symbolOrder='VGADPESLRTIQNCYHMWKF'/>
<sequence id="seq_arg_1f7u_s_cerev19A-aa" taxon="arg_1f7u_s_cerev19A-aa" totalcount="20" value="IIEFSPNIAKPFHAGHLRSTIIGGFLANLIRMNYLGDWGEFSIEKYIDTYARLDVYSGESQLYLTRDVGAAMIYVIASQQDLHAAQFFEILKQMLQHVNF----"/>
<sequence id="seq_arg_1iq0_t_therm19A-aa" taxon="arg_1iq0_t_therm19A-aa" totalcount="20" value="LVEHSVNPNKELHVGHLRNIALGDAIARILVLNYIDDTGNRILLAQMATMHALDLLVWESDTYYAKDIAFQFINVVDVRQSHPQALVRAALALAAHHLAY----"/>
<sequence id="seq_arg_2zue_p__hori18A-aa" taxon="arg_2zue_p__hori18A-aa" totalcount="20" value="IVEHSVNPTKPLHMGHARNAILGDVMARIEVQNYIDDLGEEVVRAQMVTTYKLDLLVWESDTYTGKDIAYHLINVIGAEQKHPQLAIKYALQLLLYHLAY----"/>
<sequence id="seq_arg_3fnr_c_pyl_j20A-aa" taxon="arg_3fnr_c_pyl_j20A-aa" totalcount="20" value="LLEYSANPTGPLHIGHARGAVFGDTLTRLNTEYYVNDAGDKMLVLIKQNLEQADSYVSERSTYLAADIVYHKINIWGADHHGYIPRMKAAMEFLLEIILA----"/>
<sequence id="seq_cys_1li5_e__coli1A-aa" taxon="cys_1li5_e__coli1A-aa" totalcount="20" value="GMYVGITVYDLCHIGHGRTFVAFDVVARYKYVRNITDIDDRMIAEMHKDFDALDMEPRATHGWHIECSAMNCIHGGGSDLMFPHENEIAQSTCAVYWMHS----"/>
<sequence id="seq_cys_3c8z_m__smeg17A-aa" taxon="cys_3c8z_m__smeg17A-aa" totalcount="20" value="TMYVGITPYDATHLGHAATYLTFDLVHRLQYVQNVTDVDDRETQLFREDMAALHDYVAATDGWHVECSAIALIQGGGSDLIFPHEYSAAHAESVAHYVHT----"/>
<sequence id="seq_gln_1qtq_e__coli1A-aa" taxon="gln_1qtq_e__coli1A-aa" totalcount="20" value="HTRFPPEPNGYLHIGHAKSICLNFGIAQDQCNLRFDDTNIEYVESIKNDVEWLSNVRYSSDMYDFTHCISDAHSLCTLEFQDNRRLYDWVLDNIPRQYEF----"/>
<sequence id="seq_gln_2hz7_d_radio2A-aa" taxon="gln_2hz7_d_radio2A-aa" totalcount="20" value="VTRFPPDPSGYAHLGHVFASLLDFNTARQQFNLRMDDTNQEYVDSIADDLKWLGHFYYASDAYDFEHPLQDAHSMCSLEFVDNRAIYDWLMEKLPHQYEF----"/>
<sequence id="seq_glu_1j09_t_therm16A-aa" taxon="glu_1j09_t_therm1A-aa" totalcount="20" value="VTRIAPSPTGDPHVGTAYIALFNYAWARRRFIVRIEDTDPGAEERILAALKWLDGPYRQSETYHLANVVDDHDVIRAEEWLVSTPIHVLLYRAFPRFYHM----"/>
<sequence id="seq_glu_1nzj_e__coli15A-aa" taxon="glu_1nzj_e__coli2A-aa" totalcount="20" value="IGRFAPSPSGELHFGSLIAALGSYLQARARWLVRIEDIDPGAAETILRQLEHYDDVLWQSQAYNLAVVVDDHEIVRGADLIEPTVRQISLYQLFPDYIHL----"/>
<sequence id="seq_glu_2cfo_t_elong18A-aa" taxon="glu_2cfo_t_elong3A-aa" totalcount="20" value="RVRLAPSPTGNLHIGTARTAVFNWLYARHKFILRIEDTDPEYTENILEGLQWLDGPYFQSDLYNLVVVVDDIDVIRGEDHIGNTPKQILLYEALPNFAHT----"/>
<sequence id="seq_glu_2o5r_t_itima4A-aa" taxon="glu_2o5r_t_itima4A-aa" totalcount="20" value="RVRFAPSPTGFLHVGGARTALFNFLFARKEFILRIEDTDREYEEKL?ESLRWLDGPYRQSETYNFACVVDD?HVIRGDDHLSNTLRQLALYEAFPVFAHV----"/>
<sequence id="seq_ile_1ile_t_therm19A-aa" taxon="ile_1ile_t_therm19A-aa" totalcount="20" value="TVYEPPTANGLPHVGHAQARSYKDLFPRYPRRAGWDTHGFTYEKEWEAFTERIDDAYATLEDVWYDSGAMPFFIAEGIDQTRGFNSLHQLGVMLFNVICH----"/>
<sequence id="seq_ile_1qu2_s_ureus2A-aa" taxon="ile_1qu2_s_ureus2A-aa" totalcount="20" value="ILHDPPYANGNLHMGHALNKILKDFIVRYPYVPGWDTHGLEQIELQKKDFRRLDDPYITLKDVWFDSGSSHRMYLEGSDQYRGFNSSITTSVATYFLLSH----"/>
<sequence id="seq_leu_1wz2_p__hori1A-aa" taxon="leu_1wz2_p__hori1A-aa" totalcount="20" value="YITVFPYLSGHLHVGHARTYTIPDVIARFLFPMAWHITGKYFMKAAKETFIRADREFYTTSESLSDSTIYMAWRCSGKDLIPNLTFFIFNHVAIPGIAVN----"/>
<sequence id="seq_leu_2v0c_T_thermophilus" taxon="leu_2v0c_T_thermophilus" totalcount="20" value="YVLVFPYPSGDLHMGHLKNYTMGDVLARFLHPMGWDAFGYANIRQAKESLRLMDREVTTCEDTFFDSSWYYLQYIGGVEHAVLLLYSRFFTKFLFGLFTQ----"/>
<sequence id="seq_met_1pfv_e__coli1A-aa" taxon="met_1pfv_e__coli1A-aa" totalcount="20" value="LVTCLPYANGSIHLGHMLEHIQADVWVRYNFICADDAHGGEMSQEHQTDFAGFDNYHSTHSYVWLDAPIGYMYHFIGKDIVYFSLFWPAMLEGSPNLFVH----"/>
<sequence id="seq_met_1rqg_p_byssi1A-aa" taxon="met_1rqg_p_byssi1A-aa" totalcount="20" value="MVTSLPYANGPIHAGHLAAYLPADIFVRYVFICGTDEHGDEFHEQIKITFQRADFFGRTELYVWFEAPIGYIIHFIGKDNIPFAIFWPAFLMAYPDIPAN----"/>
<sequence id="seq_met_1woy_t_therm2A-aa" taxon="met_1woy_t_therm2A-aa" totalcount="20" value="YVTTIYYVNAEPHLGHAYTTVVADFLARWFFLTGTDEHGDRVSGRFKRAWDLLDDFIRTTEFVWFDALLNYVWHLIGKDILKPAVFWPTMLKAAYHLNVG----"/>
<sequence id="seq_met_2csx_a__aeol3A-aa" taxon="met_2csx_a__aeol3A-aa" totalcount="20" value="YVTTIYYVNDVPHLGHAYTTIAADTIARYFFLTGTDEHGDRNAERFKKLWEFLTKFIRTTDYVWFDALFNYILHLVGKDILRFTVYWPAFLMSLPKVFAH----"/>
<sequence id="seq_met_2x1l_m_matis4A-aa" taxon="met_2x1l_m_matis4A-aa" totalcount="20" value="YITTIAYPNGVPHIGHAYEYIATDAIARFRYLTGTDVHGRRNSDVFQRLQEKLDRFIRTSDYVWVDALTNYLLHMIGKDIIRFTVYWPAFLMSAPRIFAH----"/>
<sequence id="seq_trp_1i6m_b_stear1A-aa" taxon="trp_1i6m_b_stear1A-aa" totalcount="20" value="TIFSGIQPSGVITIGNYIALRQFVELQHENCYFCIVDQHRQNIRRLAALYLAVATLFIQSETYPPLMAADILIVPVGEDQKQHIELTRDLAERFPEARIP----"/>
<sequence id="seq_trp_1r6u_h_h_sap19B-aa" taxon="trp_1r6u_h_h_sap19B-aa" totalcount="20" value="YLYTGRGPSSE?HVGHLIPFIFTKWLQDVPLVIQ?TDDEYGDAVENAKDIIACTFIFSDLDSFPAIQAAPSFLIPCAIDQDPYFR?TRDVAPRIPALLHS----"/>
<sequence id="seq_trp_2el7_t_therm2A-aa" taxon="trp_2el7_t_therm2A-aa" totalcount="20" value="RVLSGIQPSGEIHIGNYLAIKQWVAIGEKDAFFCIVDYHAQRTFEAALVNIAAVTLFVQSHMYPVLQAADILTVPVGEDQVQHIELTREIARRFPQALLN----"/>
<sequence id="seq_trp_2g36_t_itima4A-aa" taxon="trp_2g36_t_itima4A-aa" totalcount="20" value="RILSGMRPTGKLHIGHLVALENWVKLQEGECFYFVADWHKEYTRDLVRGFLACSVIFVQSGIYPVLQAADILGVPVGEDQVYHIELTREIARRFPEAILS----"/>
<sequence id="seq_trp_2ip1_s_cerev20A-aa" taxon="trp_2ip1_s_cerev20A-aa" totalcount="20" value="FLYTGRGPSSSMHLGHMIPFVFTKWLQEPLVIELTDDEVKNFARENAKDIIAVTFIFSDLQHFASIQIATAFLIPCAIDQDPYFRVCRDVADKLKPALLH----"/>
<sequence id="seq_try_2cyb_a__fulg20A-aa" taxon="tyr_2cyb_a__fulg20A-aa" totalcount="20" value="RAYVGYEPSGEIHLGHMMTVQKLMDLQEAEIIVLLAD-IHEVADYNKKVFIALAKFVLGSEIYPLMQALDIALAVGGIDQRKIHMLARENLPRLPVCLHT----"/>
<sequence id="seq_tyr_1h3f_t_therm18A-aa" taxon="tyr_1h3f_t_therm18A-aa" totalcount="20" value="TVKLGADPTPDLHLGHAVVLRKMRQFQELKVVLIIGD-FRENAKTYVAQAGKIFELRYNSELYPFAQAYDSVVEMGGTDQRFNLLVGREVQRAYQVCFLM----"/>
<sequence id="seq_tyr_1jil_s_ureus19A-aa" taxon="tyr_1jil_s_ureus19A-aa" totalcount="20" value="TLYCGADPTDSLHIGHLLPFLTLRRFQEHRPIVLIGG-GDKNIEGISKQMHNIAVLVNNRDTYTILQAIDFGIQVGGSDQWGNITSGIELMRRMAYGLTI----"/>
<sequence id="seq_tyr_1wq4_e__coli20A-aa" taxon="tyr_1wq4_e__coli20A-aa" totalcount="20" value="ALVCGFDPTDSLHLGHLVPLLCLKRFQQAKPVALVGG-AQEWVDKIRKQVAPFAIAANNYDSYNLLQGYDFALCIGGSDQWGNITSGIDLTRRLVFGLTV----"/>
<sequence id="seq_tyr_2cya_a_ernix17A-aa" taxon="tyr_2cya_a_ernix17A-aa" totalcount="20" value="KGYIGYEPSGVAHIGWLVWMYKVKDLVEADFSVLEAT-WHAAARIVRRVMEAAVRFVDAEEIYPLMQVSDIFIALGGMDQRKAHMLARDVAEKLPVAIHT----"/>
<sequence id="seq_tyr_2cyc_p__hori18A-aa" taxon="tyr_2cyc_p__hori18A-aa" totalcount="20" value="QHYIGFEISGYIHLGTLMAGAKIADFQKAKTRVFLAD-WHEVALYFKVGMEKSVEFVLASEIYPMMQVADIFIAHAGMDQRKAHVIAIEVAQK-PVAVHH----"/>
<sequence id="seq_tyr_2dlc_s_cerev18X-aa" taxon="tyr_2dlc_s_cerev18X-aa" totalcount="20" value="KLYWGTAPTGRPHCGYFVPMTKLADFLKAEVTVLLAD-LNYRAKYYELTIKAILKFVVGSSIYPLMQALDEQCQFGGVDQRKIFVLAEENLPSLRAHLMN----"/>
<sequence id="seq_tyr_2zp1_m_annas19A-aa" taxon="tyr_2zp1_m_annas19A-aa" totalcount="20" value="SAYIGFEPSGKIHLGHYLQIKKMIDLQNADIIILLAD-LAKIGDYNKKVFEAMAKYVYGSEIYPIMQVNTSHVAVGGMEQRKIHMLARELLP--VVCIHN----"/>
<sequence id="seq_val_1gax_t_therm17A-aa" taxon="val_1gax_t_therm17A-aa" totalcount="20" value="VIFMPPNVTGSLHMGHALDNSLQDALIRYVWLPGTDHAGEESGGTILKQLKRLDREAFTMDDTWFSSALWPLVLVTGYDILFLVSRMEVSGYHFFTVLLH----"/>
<sequence id="seq_ala_1yfsa__licus19A-aa" taxon="ala_1yfsa__licus19A-aa" totalcount="20" value="SAHEIRELFLSFFEKKGHTRVKAPLVPLFVNAGMVPFKKRATSCQKCLRVTFFEMLGNFSFKKEAIEYAWEFVTSSEIYVEIWNLVFMHPNIDTGMGLERIASV"/>
<sequence id="seq_ala_2ztg_a__fulg1A-aa" taxon="ala_2ztg_a__fulg1A-aa" totalcount="20" value="ELDE?REYYLNFFERRGHGRIEYPVVAYLTIASIADFQNPLTISQPCIRLTLFE??AHHAFKNETVAYCTELLNCLEAIVEVATLVF?NYIVDTGYGLERFVWA"/>
<sequence id="seq_ala_2zze_p__hori2A-aa" taxon="ala_2zze_p__hori2A-aa" totalcount="20" value="TLDEMRE?FLRFFE?HPHGRV-YPVLPLLVGASIMDFQNPLVISQPSIRFTIFEMMAHHAFMDETVELAFEFFTAFEVLYEVATLVFMT?VVDTGYGLERLVWM"/>
<sequence id="seq_ala_3hxv_e__coli2A-aa" taxon="ala_3hxv_e__coli2A-aa" totalcount="20" value="STAEIRQAFLDFFHSKGHQVVASSLVPLFTNAGMNQFKSRATTSQRCVRATFFEMLGNFSFKLDAILFAWLLLTCTEIFYEIWNIVFMKPSVDTGMGLERIAAV"/>
<sequence id="seq_asn_1x54a__oshii1A-aa" taxon="asn_1x54a__oshii1A-aa" totalcount="20" value="VKETLIMAAREWLLKDGWHEVFPPILVYLSQSAQLYLEEKVWSLTPSFRATEFWHLELEAALWDIMKVEEELVSASDMLAEIIGGSQRVPHSGFGLGVERLVAW"/>
<sequence id="seq_asn_3m4p_e_histo1A-aa" taxon="asn_3m4p_e_histo1A-aa" totalcount="20" value="LRSEIQWYFRKYYHDNHFTEIQPPTIVYLTQSSQLYLEGKSFCMLSSYRAAEYLHLEAELPFEDLLNHLEDLVCSVDLLMEIVGGSMRCPHGGYGLGVERLVMW"/>
<sequence id="seq_asn_d1asza_therm1A-aa" taxon="asn_d1asza_therm1A-aa" totalcount="20" value="IQAGVCELFREYLATKKFTEVHTPKLLYLAQSPQFNKQERVYEIGPVFRATEFTGLDMEMAYHEVLDTLSELFVSYDFFMEILSGAQRPPHAGGGIGLERVVMF"/>
<sequence id="seq_asp_1wydb__odaii1B-aa" taxon="asp_1wydb__odaii1B-aa" totalcount="20" value="IQSLALKAFRETLYKEGFIEIFTPKIIFLAQSPQLYKEERVFEVAPAWRAAEFISMDVEMAYNDVMQLLEKILHSFDLIYEIVSGSTRPPHAGFGMGLARLMVM"/>
<sequence id="seq_asp_3i7f_e_ytica1A-aa" taxon="asp_3i7f_e_ytica1A-aa" totalcount="20" value="IQSACCGLFREFLTSQKFVEIHTPKLIYLAQSPQLYKQRKVFEVGPVFRATEFEGLDIEMEYHECIDVMEKLFTSYDVFVEITSGAQRWPHAGCGIGLERITML"/>
<sequence id="seq_asp_d1b8aa_ensis2A-aa" taxon="asp_d1b8aa_ensis2A-aa" totalcount="20" value="IRSSVFKAVRDFFHENGFIEIHTPKIIFLAESPQLYKEDRVYEIAPIFRANEAWSIDSEMAEEEVMSFLERLVAAFDLEYEISSGGQRPPHGGFGLGAERLIKQ"/>
<sequence id="seq_asp_d1c0aa__coli1A-aa" taxon="asp_d1c0aa__coli1A-aa" totalcount="20" value="TRAKITSLVRRFMDDHGFLDIETPMLTALPQSPQLFKQDRYYQIVKCFRDPEFTQIDVETSAPQVREVMEALVRAYDMVIEVGGGSVRPPHAGLAFGLDRLTML"/>
<sequence id="seq_asp_d1efwa_therm2A-aa" taxon="asp_d1efwa_therm2A-aa" totalcount="20" value="LRHRVIKAIWDFLDREGFVQVETPFLTALPQSPQLFKQDRYFQIARCFRDPDFTQLDLEMSVEDVLELNERLMAAYDLVLEVGGGSIRPPHGGIAWGLDRLLAL"/>
<sequence id="seq_gly_2zt5_h_h_sap1A-aa" taxon="gly_2zt5_h_h_sap1A-aa" totalcount="20" value="LKNNIIQTWRQHFQEEQILEIDCTMLTYLRPETAQGIFFAAAQIGNSFRNREFTMAEIEHFLGYFIGRIYLYLTCWDAESEIVGCADRPNVIEPSFGLGRIMYT"/>
<sequence id="seq_gly_d1atib_therm2A-aa" taxon="gly_d1atib_therm2A-aa" totalcount="20" value="LKNNLKQAWWRRNVERDMEGLDASVLTYLRPETAQGIFFGIAQIGKAFRNREFEQMEIEYFHRYWVEERLKWWQTVDILYELEGIAQRPYVIEPSAGVDRGVLA"/>
<sequence id="seq_gly_d1j5wb_itima3A-aa" taxon="gly_d1j5wb_itima3A-aa" totalcount="20" value="YLQDVI-KLNDFWASKGCLLEQYDE----VGAGTFHTFWKVAYVQPSRRPQRYFQYQVIIKPENSQELYLESLEGWEVWLEITQFTYFDIPLEITYGLERIA-Y"/>
<sequence id="seq_his_1htt_e__coli18A-aa" taxon="his_1htt_e__coli1A-aa" totalcount="20" value="IWQRIEGTLKNVLGSYGYSEIRLPIVETLRPEGTAGCVQRLWYIGPMFRHRQFHQLGCEVFDAELIMLTARWWRVFEWVTTVCAGGRYTPAVGFAMGLERLVLL"/>
<sequence id="seq_his_1wu7a___acid1A-aa" taxon="his_1wu7a___acid1A-aa" totalcount="20" value="VEKFIFKTAEEAAEAFGFRRIDFPSLETLIPEATPSTVLRWYSFPKVWRYREHYQFNADIFDAEVIALASSILDVFEAYDAILGGGRYVPAVGFG?GDAVISLL"/>
<sequence id="seq_his_3hri_t_rucei1A-aa" taxon="his_3hri_t_rucei1A-aa" totalcount="20" value="LRKYLFDVFHSTARKFGFEEYDSPVLEALRPEMTPSLAAKWYSIPQCWRYREHYQWNMDIIEVELVCAACTAMQVFEGFDALCGGGRYVPCVGFGFGDCVIVEL"/>
<sequence id="seq_his_3lc0_t_cruzi2A-aa" taxon="his_3lc0_t_cruzi2A-aa" totalcount="20" value="CRRHLFDVFHATAKTFGFEEYDAPVLEALRPEMTPSLAAKWYSIPQCWRYREHYQWNMDIVEVELVCAACWAMRVFEGFDALCGGGRYIPCAGFGFGDCVIVEL"/>
<sequence id="seq_his_d1adjc_therm20A-aa" taxon="his_d1adjc_therm2A-aa" totalcount="20" value="MHQRIVATARKVLEAAGALELVTPIFETLRPEGTAAMVVRLWMAGPMFRARQFHQVNYEALDAEAVVLLYECLKAFEVHHALGGGGRYVPGVGFAFGVERVALA"/>
<sequence id="seq_his_d1qe0a_aureu3A-aa" taxon="his_d1qe0a_aureu3A-aa" totalcount="20" value="KWRYIENQLDELMTFYNYKEIRTPIFETLRPEGTAAVVIKLYYNGPMFRYRQFNQFGVEAIDAEVLAMVMHIYQAFELMMTLCGGGRYETGIGFALSIERLLLA"/>
<sequence id="seq_lys_3bju___piens1A-aa" taxon="lys_3bju___piens1A-aa" totalcount="20" value="IRSKIITYIRSFLDELGFLEIETPMMNYMRIAPELYHKDRVYEIGRQFRNPEFTTCEFYMAYHDLMEITEKMVSRFELFVEICNAYTEPPTAGWGMGIDRVAMF"/>
<sequence id="seq_lys_3e9h_b_stear3A-aa" taxon="lys_3e9h_b_stear3A-aa" totalcount="20" value="TRSLIIQSMRRYLDSHGYLEVETPMMHYMRIAIELHLKEKVYEIGRVFRNPEFTMLELYEAFRDIMKLTENLIARFELFIEHANAFTEPPTGGLGIGVDRLVML"/>
<sequence id="seq_lys_3g1z_s_urium2A-aa" taxon="lys_3g1z_s_urium2A-aa" totalcount="20" value="KRAAIMAEIRRFFADRGVLEVETPCMSYLMTSPEYHMKGPVFQLCRSFRNPEFTMLEWYRPMYRLMNEVDDLLQRFEVYYELANGFHEPDCSGVALGVDRLVML"/>
<sequence id="seq_lys_d1e1oa__coli1A-aa" taxon="lys_d1e1oa__coli1A-aa" totalcount="20" value="VRSKILAAIRQFMVARGFMEVETPMMQYLRIAPELYLKERVFEINRNFRNPEFTMMELYMAYHDLIELTESLFRRFEFFIEIGNGFSEPPTAGLGIGIDRMIML"/>
<sequence id="seq_phe_2alya__therm1A-aa" taxon="phe_2alya__therm1A-aa" totalcount="20" value="PITLMERELVEIFRALGYQAVEGPEVELLRTHTSPMQVFRIVVPGRVFRFAVFHQLEGLVVMAHLKGAIYELAQGAQFAVELGGAGMVVTGFAFGLGVERLAML"/>
<sequence id="seq_phe_2rhq_s_cus_a2A-aa" taxon="phe_2rhq_s_cus_a2A-aa" totalcount="20" value="PLTRTVEEIEDLFLGLGYEIVDGYEVELMRTHTSPVQAVKIICPGKVYRRHQFTQIEGLVVMSDLKGTLELVAKSVEVDVEILGAGMVYSGFAFGMGPDRIAML"/>
<sequence id="seq_phe_3l4g_h_h_sap1A-aa" taxon="phe_3l4g_h_h_sap1A-aa" totalcount="20" value="PLLKVRSQFRQIFLEMGFTEMPTNFIELLRTHTTSASAVKYFSIDRVFRNAEFHQIEGVVALGHLMGVLREFFTSMEVFSEVGNSGVFVSVIAWGLSLERPTMI"/>
<sequence id="seq_pro_2i4la__stris20A-aa" taxon="pro_2i4la__stris20A-aa" totalcount="20" value="VLKKIEQIVREEQNRAGAIELLMPTLQLYGPTNEEMITLNLYHIQWKFRDREFLMKDAYSFYNKMFVAYLRTFASHEFIVEVGQIFYFIHGGSYGVGVSRLLGA"/>
<sequence id="seq_pro_2j3mb__calis19B-aa" taxon="pro_2j3mb__calis19B-aa" totalcount="20" value="VLEKLKTIMREEFEKIDAVEMLMPALLILGPTHEETFTLNLYQIQTKYRDREFIMKDGYSFYRDYEKAYSRIFESKEFMAEIGHIFKLVIMGCYGIGVSRLLSA"/>
<sequence id="seq_pro_3ial_g__lamb1A-aa" taxon="pro_3ial_g__lamb1A-aa" totalcount="20" value="MENAIMRLCEEEYAKVGISQILFPTVIALRPTSETAIYLKIHQTCTIFRHREIHWNEAHCCLSDYWKVIDTIFSSEVSDVQTAGIHNLPYLTCAGIS-TRVLAC"/>
<sequence id="seq_pro_d1hc7a_therm18A-aa" taxon="pro_d1hc7a_therm18A-aa" totalcount="20" value="IWENIQQVLDRMFKETGHQNAYFPLFIAVRPTSETVIGQLLNQWGNVVRWSEFLWQEGHTAVRRMLSIYARLARTTTIEAQAGTSHYLVHTTSWGLS-WRFIGA"/>
<sequence id="seq_pro_d1nj1a_therm2A-aa" taxon="pro_d1nj1a_therm2A-aa" totalcount="20" value="IRKNTLKILRRILDR-DHEEVLFPLLVALRPTSETVMYMRFYQVVNTFRYREITFKEAHTIVERAVEIYKEFFNTVAFDTQIGTVHNLVHQTCYGLS-DRVIAS"/>
<sequence id="seq_pro_d1nj8a_janas1A-aa" taxon="pro_d1nj8a_janas1A-aa" totalcount="20" value="IRRYTFEIIRNLLDESGHDEALFPMLIALRPTSETPIYIKIYQIVNTFRYREITFKEAHTAVKEAISIYKKFFDTMAFDTQIATVHNLAYQTCYGIS-DRVIAS"/>
<sequence id="seq_ser_1wleb__aurus19B-aa" taxon="ser_1wleb__aurus19B-aa" totalcount="20" value="LQHGLVNFTLNKLIHRGFTPMTVPDLLNLAGTAEVGLAIRMVCSSTCYRAHHFTKVEMFGVLEEFLSLQMEILTKFDIEAEVTSASNCAHTVNATGAVPRLLIA"/>
<sequence id="seq_ser_2cjab__rkeri2B-aa" taxon="ser_2cjab__rkeri2B-aa" totalcount="20" value="IFRTFEKIVLEELEPLGYRE?IFPKLVG?CYAQCPPFWVKVFDRSTSHRYDEFHRIEIVWIAEELHDRY?HIFNTTDYEAEFQNVSINLWSGCSGVGLERWAAV"/>
<sequence id="seq_ser_d1sera_therm1A-aa" taxon="ser_d1sera_therm20A-aa" totalcount="20" value="YELALLRFAMDFMARRGFLPMTLPSYAYLTGTAEVVLNLRYAGYAPAFRSHQFHKVEQYVLFQELLENAEEILRQVDIEVETHSCSALAYTLNNTAATPRILAM"/>
<sequence id="seq_thr_3a32_a_ernix20A-aa" taxon="thr_3a32_a_ernix20A-aa" totalcount="20" value="IRYALAEVLAKFHARRGYYVVETPIIAAVKPMNCPYHIFKVFEFGRVHRYRGFTQDDAHIIVYDVFEEMKLVLEKLDFIMQMGTIQFDVYIIHRALSIERFLGV"/>
<sequence id="seq_thr_d1evka__coli20A-aa" taxon="thr_d1evka__coli20A-aa" totalcount="20" value="IFRELEVFVRSKLKEYQYQEVKGPFMMCIKPMNCPGHVLRMAEFGSCHRNRGFTQDDAHIFVNGCIRLVYDMYSKIEFTLQCGTVQLDPVMIHRAISMERFIGI"/>
<sequence id="seq_thr_d1nyra_ureus19A-aa" taxon="thr_d1nyra_ureus19A-aa" totalcount="20" value="IRREIERYIVDKEVSMGYDHVYTPVLAVLRPMNCPHHMIRIAELGTMHRYRGMTLNDSHIFFKRVVNMIIDVYKKLDVQVTLSTAQLDPVVIHRGVTMERFVAF"/>
</data>
<map name="Beta">beast.math.distributions.Beta</map>
<map name="Exponential">beast.math.distributions.Exponential</map>
<map name="InverseGamma">beast.math.distributions.InverseGamma</map>
<map name="LogNormal">beast.math.distributions.LogNormalDistributionModel</map>
<map name="Gamma">beast.math.distributions.Gamma</map>
<map name="Uniform">beast.math.distributions.Uniform</map>
<map name="prior">beast.math.distributions.Prior</map>
<map name="LaplaceDistribution">beast.math.distributions.LaplaceDistribution</map>
<map name="OneOnX">beast.math.distributions.OneOnX</map>
<map name="Normal">beast.math.distributions.Normal</map>
<map name="taxon">beast.evolution.alignment.Taxon</map>
<map name="taxonset">beast.evolution.alignment.TaxonSet</map>
<taxonset id='allTaxa' alignment='@AARS'/>
<run chainLength="10000000" id="mcmc" spec="MCMC">
<state id="state" storeEvery="5000">
<tree id="Tree.t:AARS" name="stateNode">
<taxonset id="TaxonSet.AARS" spec="TaxonSet">
<data idref="AARS" name="alignment"/>
</taxonset>
</tree>
<parameter id="birthRate.t:AARS" name="stateNode" value="1.0"/>
<stateNode idref='ucldStdev.c:AARS'/>
<stateNode idref='rateCategories.c:AARS'/>
</state>
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="prior" spec="util.CompoundDistribution">
<distribution id="V.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="V" spec="TaxonSet">
<taxon id="val_1gax_t_therm17A-aa"/>
</taxonset>
</distribution>
<distribution id="G.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="G" spec="TaxonSet">
<taxon id="gly_d1atib_therm2A-aa"/>
<taxon id="gly_d1j5wb_itima3A-aa"/>
<taxon id="gly_2zt5_h_h_sap1A-aa"/>
</taxonset>
</distribution>
<distribution id="A.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="A" spec="TaxonSet">
<taxon id="ala_1yfsa__licus19A-aa"/>
<taxon id="ala_3hxv_e__coli2A-aa"/>
<taxon id="ala_2ztg_a__fulg1A-aa"/>
<taxon id="ala_2zze_p__hori2A-aa"/>
</taxonset>
</distribution>
<distribution id="D.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="D" spec="TaxonSet">
<taxon id="asp_1wydb__odaii1B-aa"/>
<taxon id="asp_d1b8aa_ensis2A-aa"/>
<taxon id="asp_d1c0aa__coli1A-aa"/>
<taxon id="asp_d1efwa_therm2A-aa"/>
<taxon id="asp_3i7f_e_ytica1A-aa"/>
</taxonset>
</distribution>
<distribution id="P.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="P" spec="TaxonSet">
<taxon id="pro_d1nj8a_janas1A-aa"/>
<taxon id="pro_2i4la__stris20A-aa"/>
<taxon id="pro_2j3mb__calis19B-aa"/>
<taxon id="pro_d1hc7a_therm18A-aa"/>
<taxon id="pro_d1nj1a_therm2A-aa"/>
<taxon id="pro_3ial_g__lamb1A-aa"/>
</taxonset>
</distribution>
<distribution id="E.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="E" spec="TaxonSet">
<taxon id="glu_1j09_t_therm1A-aa"/>
<taxon id="glu_1nzj_e__coli2A-aa"/>
<taxon id="glu_2cfo_t_elong3A-aa"/>
<taxon id="glu_2o5r_t_itima4A-aa"/>
</taxonset>
</distribution>
<distribution id="S.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="S" spec="TaxonSet">
<taxon id="ser_d1sera_therm20A-aa"/>
<taxon id="ser_1wleb__aurus19B-aa"/>
<taxon id="ser_2cjab__rkeri2B-aa"/>
</taxonset>
</distribution>
<distribution id="L.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="L" spec="TaxonSet">
<taxon id="leu_1wz2_p__hori1A-aa"/>
<taxon id="leu_2v0c_T_thermophilus"/>
</taxonset>
</distribution>
<distribution id="R.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="R" spec="TaxonSet">
<taxon id="arg_2zue_p__hori18A-aa"/>
<taxon id="arg_1iq0_t_therm19A-aa"/>
<taxon id="arg_3fnr_c_pyl_j20A-aa"/>
<taxon id="arg_1f7u_s_cerev19A-aa"/>
</taxonset>
</distribution>
<distribution id="T.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="T" spec="TaxonSet">
<taxon id="thr_3a32_a_ernix20A-aa"/>
<taxon id="thr_d1evka__coli20A-aa"/>
<taxon id="thr_d1nyra_ureus19A-aa"/>
</taxonset>
</distribution>
<distribution id="I.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="I" spec="TaxonSet">
<taxon id="ile_1ile_t_therm19A-aa"/>
<taxon id="ile_1qu2_s_ureus2A-aa"/>
</taxonset>
</distribution>
<distribution id="Q.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="Q" spec="TaxonSet">
<taxon id="gln_1qtq_e__coli1A-aa"/>
<taxon id="gln_2hz7_d_radio2A-aa"/>
</taxonset>
</distribution>
<distribution id="N.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="N" spec="TaxonSet">
<taxon id="asn_1x54a__oshii1A-aa"/>
<taxon id="asn_d1asza_therm1A-aa"/>
<taxon id="asn_3m4p_e_histo1A-aa"/>
</taxonset>
</distribution>
<distribution id="C.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="C" spec="TaxonSet">
<taxon id="cys_3c8z_m__smeg17A-aa"/>
<taxon id="cys_1li5_e__coli1A-aa"/>
</taxonset>
</distribution>
<distribution id="Y.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="Y" spec="TaxonSet">
<taxon id="tyr_2cyb_a__fulg20A-aa"/>
<taxon id="tyr_2cya_a_ernix17A-aa"/>
<taxon id="tyr_2cyc_p__hori18A-aa"/>
<taxon id="tyr_2zp1_m_annas19A-aa"/>
<taxon id="tyr_1h3f_t_therm18A-aa"/>
<taxon id="tyr_1jil_s_ureus19A-aa"/>
<taxon id="tyr_1wq4_e__coli20A-aa"/>
<taxon id="tyr_2dlc_s_cerev18X-aa"/>
</taxonset>
</distribution>
<distribution id="H.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="H" spec="TaxonSet">
<taxon id="his_1htt_e__coli1A-aa"/>
<taxon id="his_d1adjc_therm2A-aa"/>
<taxon id="his_d1qe0a_aureu3A-aa"/>
<taxon id="his_3hri_t_rucei1A-aa"/>
<taxon id="his_3lc0_t_cruzi2A-aa"/>
<taxon id="his_1wu7a___acid1A-aa"/>
</taxonset>
</distribution>
<distribution id="M.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="M" spec="TaxonSet">
<taxon id="met_1rqg_p_byssi1A-aa"/>
<taxon id="met_1pfv_e__coli1A-aa"/>
<taxon id="met_1woy_t_therm2A-aa"/>
<taxon id="met_2csx_a__aeol3A-aa"/>
<taxon id="met_2x1l_m_matis4A-aa"/>
</taxonset>
</distribution>
<distribution id="W.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="W" spec="TaxonSet">
<taxon id="trp_1i6m_b_stear1A-aa"/>
<taxon id="trp_2el7_t_therm2A-aa"/>
<taxon id="trp_2g36_t_itima4A-aa"/>
<taxon id="trp_1r6u_h_h_sap19B-aa"/>
<taxon id="trp_2ip1_s_cerev20A-aa"/>
</taxonset>
</distribution>
<distribution id="K.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="K" spec="TaxonSet">
<taxon id="lys_3e9h_b_stear3A-aa"/>
<taxon id="lys_3g1z_s_urium2A-aa"/>
<taxon id="lys_d1e1oa__coli1A-aa"/>
<taxon id="lys_3bju___piens1A-aa"/>
</taxonset>
</distribution>
<distribution id="F.prior" monophyletic="true" spec="beast.math.distributions.MRCAPrior" tree="@Tree.t:AARS">
<taxonset id="F" spec="TaxonSet">
<taxon id="phe_2alya__therm1A-aa"/>
<taxon id="phe_2rhq_s_cus_a2A-aa"/>
<taxon id="phe_3l4g_h_h_sap1A-aa"/>
</taxonset>
</distribution>
<distribution spec='beast.evolution.substitutionmodel.AARSTreePrior' id='AARSprior'>
<trait id="TraitSet1" spec="beast.evolution.tree.TraitSet" taxa="@allTaxa" traitname="state" units="year">
val_1gax_t_therm17A-aa=0,
gly_d1atib_therm2A-aa=1,
gly_d1j5wb_itima3A-aa=1,
gly_2zt5_h_h_sap1A-aa=1,
ala_1yfsa__licus19A-aa=2,
ala_3hxv_e__coli2A-aa=2,
ala_2ztg_a__fulg1A-aa=2,
ala_2zze_p__hori2A-aa=2,
asp_1wydb__odaii1B-aa=3,
asp_d1b8aa_ensis2A-aa=3,
asp_d1c0aa__coli1A-aa=3,
asp_d1efwa_therm2A-aa=3,
asp_3i7f_e_ytica1A-aa=3,
pro_d1nj8a_janas1A-aa=4,
pro_2i4la__stris20A-aa=4,
pro_2j3mb__calis19B-aa=4,
pro_d1hc7a_therm18A-aa=4,
pro_d1nj1a_therm2A-aa=4,
pro_3ial_g__lamb1A-aa=4,
glu_1j09_t_therm1A-aa=5,
glu_1nzj_e__coli2A-aa=5,
glu_2cfo_t_elong3A-aa=5,
glu_2o5r_t_itima4A-aa=5,
ser_d1sera_therm20A-aa=6,
ser_1wleb__aurus19B-aa=6,
ser_2cjab__rkeri2B-aa=6,
leu_1wz2_p__hori1A-aa=7,
leu_2v0c_T_thermophilus=7,
arg_2zue_p__hori18A-aa=8,
arg_1iq0_t_therm19A-aa=8,
arg_3fnr_c_pyl_j20A-aa=8,
arg_1f7u_s_cerev19A-aa=8,
thr_3a32_a_ernix20A-aa=8,
thr_d1evka__coli20A-aa=8,
thr_d1nyra_ureus19A-aa=8,
ile_1ile_t_therm19A-aa=9,
ile_1qu2_s_ureus2A-aa=9,
gln_1qtq_e__coli1A-aa=10,
gln_2hz7_d_radio2A-aa=10,
asn_1x54a__oshii1A-aa=11,
asn_d1asza_therm1A-aa=11,
asn_3m4p_e_histo1A-aa=11,
cys_3c8z_m__smeg17A-aa=12,
cys_1li5_e__coli1A-aa=12,
tyr_2cyb_a__fulg20A-aa=13,
tyr_2cya_a_ernix17A-aa=13,
tyr_2cyc_p__hori18A-aa=13,
tyr_2zp1_m_annas19A-aa=13,
tyr_1h3f_t_therm18A-aa=13,
tyr_1jil_s_ureus19A-aa=13,
tyr_1wq4_e__coli20A-aa=13,
tyr_2dlc_s_cerev18X-aa=13,
his_1htt_e__coli1A-aa=14,
his_d1adjc_therm2A-aa=14,
his_d1qe0a_aureu3A-aa=14,
his_3hri_t_rucei1A-aa=14,
his_3lc0_t_cruzi2A-aa=14,
his_1wu7a___acid1A-aa=14,
met_1rqg_p_byssi1A-aa=15,
met_1pfv_e__coli1A-aa=15,
met_1woy_t_therm2A-aa=15,
met_2csx_a__aeol3A-aa=15,
met_2x1l_m_matis4A-aa=15,
trp_1i6m_b_stear1A-aa=16,
trp_2el7_t_therm2A-aa=16,
trp_2g36_t_itima4A-aa=16,
trp_1r6u_h_h_sap19B-aa=16,
trp_2ip1_s_cerev20A-aa=16,
lys_3e9h_b_stear3A-aa=17,
lys_3g1z_s_urium2A-aa=17,
lys_d1e1oa__coli1A-aa=17,
lys_3bju___piens1A-aa=17,
phe_2alya__therm1A-aa=19,
phe_2rhq_s_cus_a2A-aa=19,
phe_3l4g_h_h_sap1A-aa=19
</trait>
<treeIntervals id='treeIntervals' spec='beast.evolution.tree.coalescent.TreeIntervals' tree='@Tree.t:AARS'/>
</distribution>
<distribution birthDiffRate="@birthRate.t:AARS" id="YuleModel.t:AARS" spec="beast.evolution.speciation.YuleModel" tree="@Tree.t:AARS"/>
<prior id="YuleBirthRatePrior.t:AARS" name="distribution" x="@birthRate.t:AARS">
<Uniform id="Uniform.0" name="distr" upper="Infinity"/>
</prior>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution">
<distribution data="@AARS" id="treeLikelihood.AARS" spec="ThreadedTreeLikelihood" tree="@Tree.t:AARS">
<siteModel id="SiteModel.s:AARS" spec="SiteModel">
<parameter estimate="false" id="mutationRate.s:AARS" name="mutationRate" value="1.0"/>
<parameter estimate="false" id="gammaShape.s:AARS" name="shape" value="1.0"/>
<parameter estimate="false" id="proportionInvariant.s:AARS" lower="0.0" name="proportionInvariant" upper="1.0" value="0.0"/>
<substModel id="substmodel" spec="TriStateAARSSubstitutionModel" tree="@Tree.t:AARS">
<trait idref="TraitSet1"/>
<defaultModel spec='GeneralSubstitutionModel' rates='
0.18727491 2.0069284065 0.1526315789 0.5886402754 1.8004640371 0.3144104803 0.2330935252 1.3885245902 0.2522727273 7.8164948454 0.3024523161 1 0.3144475921 0.1969309463 2.0564102564 0.118852459 0.3680555556 0.3048387097 0.6510416667
0.1875881523 1.4168591224 0.8666666667 0.5679862306 0.0614849188 0.2423580786 1.3424460432 0.2262295082 0.5840909091 0.0309278351 0.3297002725 0.3056994819 0.104815864 1.1253196931 0.1743589744 0.25 0.3333333333 0.3741935484 0.0494791667
2.0056417489 1.4153661465 0.7403508772 1.5817555938 0.3979118329 1.4366812227 3.3712230216 2.1213114754 0.5522727273 0.193814433 0.9100817439 1.0259067358 0.2407932011 0.5089514066 0.8923076923 0.3155737705 0.1111111111 0.9064516129 0.2109375
0.1523272214 0.8655462185 0.7390300231 6.1703958692 0.0846867749 0.423580786 1.071942446 0.3754098361 0.1477272727 0.0391752577 0.6185286104 0.0310880829 0.3257790368 5.4271099744 0.1025641026 0.9303278689 0.1319444444 0.4806451613 0.046875
0.5881523272 0.5678271309 1.5831408776 6.1789473684 0.1542923434 0.6812227074 0.7050359712 0.8229508197 0.4386363636 0.1278350515 5.4741144414 0.0207253886 0.1954674221 0.9462915601 0.3128205128 0.5696721311 0.1597222222 2.585483871 0.0807291667
1.7997179126 0.0612244898 0.3983833718 0.0842105263 0.1549053356 0.4148471616 0.345323741 0.3262295082 0.4977272727 3.1690721649 0.8692098093 0.3834196891 0.3994334278 0.1304347826 4.8564102564 0.5 0.6666666667 0.2580645161 2.1171875
0.3145275035 0.243697479 1.4387990762 0.4245614035 0.6815834768 0.4153132251 1.6143884892 0.7950819672 0.6795454545 0.0989690722 0.9346049046 0.1088082902 0.2152974504 0.1943734015 0.1692307692 0.6967213115 0.1388888889 0.5564516129 0.1614583333
0.2327221439 1.3409363745 3.3718244804 1.0719298246 0.7039586919 0.3445475638 1.6113537118 4.3786885246 1.2227272727 0.3195876289 1.029972752 1.4093264249 0.7875354108 3.9744245524 0.4923076923 0.7418032787 0.5208333333 0.9677419355 0.546875
1.3878702398 0.2256902761 2.1212471132 0.3754385965 0.8227194492 0.3271461717 0.7947598253 4.3798561151 0.5545454545 1.4577319588 0.8583106267 0.5129533679 0.2917847025 2.0306905371 1.5179487179 0.4754098361 0.1111111111 1.3870967742 0.171875
0.2524682652 0.5846338535 0.5519630485 0.1473684211 0.4388984509 0.4976798144 0.6790393013 1.2244604317 0.5540983607 0.187628866 3.038147139 0.5284974093 0.3824362606 0.6342710997 0.6820512821 2.1393442623 1.1597222222 5.3532258065 0.1015625
7.8208744711 0.0300120048 0.1928406467 0.0385964912 0.1273666093 3.1716937355 0.1004366812 0.3194244604 1.4590163934 0.1863636364 0.1144414169 0.170984456 0.4192634561 0.5549872123 4.2564102564 0.1393442623 0.2152777778 0.3241935484 1.0598958333
0.3018335684 0.3301320528 0.9087759815 0.6175438596 5.4664371773 0.8700696056 0.9323144105 1.0287769784 0.8573770492 3.0340909091 0.1134020619 0.0984455959 0.2266288952 1.5421994885 1.5435897436 4.2991803279 0.2152777778 3.8967741935 0.0989583333
1.0014104372 0.306122449 1.0277136259 0.0298245614 0.0206540448 0.3839907193 0.1091703057 1.4086330935 0.5131147541 0.5272727273 0.1690721649 0.0980926431 0.5439093484 0.2659846547 0.3897435897 0.25 0.7152777778 0.0741935484 0.3984375
0.3145275035 0.1032412965 0.2413394919 0.3263157895 0.1962134251 0.3990719258 0.2161572052 0.7870503597 0.2918032787 0.3818181818 0.4206185567 0.2288828338 0.5440414508 1.0869565217 0.4307692308 3.8770491803 2.4861111111 0.1338709677 6.4609375
0.1960507757 1.12484994 0.5103926097 5.4333333333 0.9466437177 0.1310904872 0.1943231441 3.9755395683 2.031147541 0.6340909091 0.5546391753 1.5449591281 0.2642487047 1.0849858357 0.2 3.9631147541 0.0694444444 3.0129032258 0.0963541667
2.0578279267 0.1740696279 0.8937644342 0.1035087719 0.3149741824 4.8549883991 0.1703056769 0.4935251799 1.5163934426 0.6818181818 4.2536082474 1.5476839237 0.3886010363 0.4277620397 0.1969309463 0.4057377049 0.5138888889 0.935483871 1.1927083333
0.1184767278 0.24969988 0.317551963 0.9315789474 0.569707401 0.5 0.6965065502 0.7410071942 0.4737704918 2.1363636364 0.1381443299 4.2970027248 0.2487046632 3.8696883853 3.9539641944 0.4051282051 0.2638888889 0.8903225806 0.6796875
0.365303244 0.337334934 0.1131639723 0.1298245614 0.156626506 0.6658932715 0.1397379913 0.5237410072 0.1114754098 1.1636363636 0.212371134 0.2152588556 0.7150259067 2.4844192635 0.0716112532 0.5179487179 0.262295082 0.1370967742 1.53125
0.3060648801 0.3733493397 0.9064665127 0.4807017544 2.5817555938 0.2575406032 0.556768559 0.9669064748 1.3868852459 5.3477272727 0.3237113402 3.8991825613 0.0725388601 0.1331444759 3.010230179 0.9333333333 0.893442623 0.1388888889 0.0885416667
0.6502115656 0.0504201681 0.2101616628 0.0473684211 0.0808950086 2.1148491879 0.1615720524 0.5467625899 0.1721311475 0.1022727273 1.0577319588 0.1008174387 0.3989637306 6.4504249292 0.0971867008 1.1897435897 0.6803278689 1.5277777778 0.0887096774
'>
<frequencies spec='Frequencies' frequencies='0.0709 0.0833 0.0866 0.057 0.0581 0.0862 0.0458 0.0695 0.061 0.044 0.0485 0.0367 0.0193 0.0353 0.0391 0.0195 0.0244 0.0144 0.062 0.0384
'/>
</defaultModel>
<frequencies estimate="true" id="AARSFrequencies0" spec="AARSFrequencies">
<parameter dimension="1" estimate="true" id="RealParameter0" name="frequencies" value="1 0 0"/>
</frequencies>
</substModel>
</siteModel>
<branchRateModel spec='beast.evolution.branchratemodel.UCRelaxedClockModel' id="RelaxedClock.c:AARS" tree='@Tree.t:AARS'>
<parameter name='clock.rate' id='ucldMean.c:AARS' value='1.0'/>
<distr id='LogNormalDistributionModel.c:AARS' name='distr' spec="beast.math.distributions.LogNormalDistributionModel" meanInRealSpace='true'>
<parameter name='M' value="1.0" estimate='false' lower='0' upper='1'/>
<parameter name='S' id='ucldStdev.c:AARS' value="0.5" lower="0" upper="1" estimate='true'/>
</distr>
<rateCategories spec='parameter.IntegerParameter' id='rateCategories.c:AARS' value="1" dimension='10' estimate='true'/>
</branchRateModel>
</distribution>
</distribution>
</distribution>
<operator id='ucldStdevScaler.c:AARS' spec='ScaleOperator' scaleAll='false' scaleFactor="0.5" weight="3" parameter="@ucldStdev.c:AARS"/>
<operator id="CategoriesRandomWalk.c:AARS" spec="IntRandomWalkOperator" windowSize='1' weight="10" parameter="@rateCategories.c:AARS"/>
<operator id='CategoriesSwapOperator.c:AARS' spec='SwapOperator' howMany="1" weight="10" intparameter='@rateCategories.c:AARS'/>
<operator id='CategoriesUniform.c:AARS' spec='UniformOperator' weight="10" parameter='@rateCategories.c:AARS'/>
<operator id="YuleBirthRateScaler.t:AARS" parameter="@birthRate.t:AARS" scaleFactor="0.75" spec="ScaleOperator" weight="3.0"/>
<operator id="treeScaler.t:AARS" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:AARS" weight="3.0"/>
<operator id="treeRootScaler.t:AARS" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:AARS" weight="3.0"/>
<operator id="UniformOperator.t:AARS" spec="Uniform" tree="@Tree.t:AARS" weight="30.0"/>
<operator id="SubtreeSlide.t:AARS" spec="SubtreeSlide" tree="@Tree.t:AARS" weight="15.0"/>
<operator id="narrow.t:AARS" spec="Exchange" tree="@Tree.t:AARS" weight="15.0"/>
<operator id="wide.t:AARS" isNarrow="false" spec="Exchange" tree="@Tree.t:AARS" weight="3.0"/>
<operator id="WilsonBalding.t:AARS" spec="WilsonBalding" tree="@Tree.t:AARS" weight="3.0"/>
<operator id='RestrictedSubtreeSlide' spec='RestrictedSubtreeSlide' weight='60' tree='@Tree.t:AARS'>
<clade idref='V'/>
<clade idref='G'/>
<clade idref='A'/>
<clade idref='D'/>
<clade idref='P'/>
<clade idref='E'/>
<clade idref='S'/>
<clade idref='L'/>
<clade idref='R'/>
<clade idref='T'/>
<clade idref='I'/>
<clade idref='Q'/>
<clade idref='N'/>
<clade idref='C'/>
<clade idref='Y'/>
<clade idref='H'/>
<clade idref='M'/>
<clade idref='W'/>
<clade idref='K'/>
<clade idref='F'/>
</operator>
<logger fileName="AARS.log" id="tracelog" logEvery="10000" model="@posterior" sanitiseHeaders="true" sort="smart">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="treeLikelihood.AARS"/>
<log id="TreeHeight.t:AARS" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:AARS"/>
<log idref="YuleModel.t:AARS"/>
<parameter idref="birthRate.t:AARS" name="log"/>
<log id='rate.c:AARS' spec='beast.evolution.branchratemodel.RateStatistic' tree='@Tree.t:AARS' branchratemodel='@RelaxedClock.c:AARS'/>
<log idref='ucldStdev.c:AARS'/>
</logger>
<logger id="screenlog" logEvery="1000">
<log idref="posterior"/>
<log arg="@posterior" id="ESS.0" spec="util.ESS"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger fileName="AARS.trees" id="treelog.t:AARS" logEvery="10000" mode="tree">
<log id="TreeWithMetaDataLogger.t:AARS" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:AARS"/>
</logger>
<init estimate="false" id="TreeParser.t:AARS" initial="@Tree.t:AARS" spec="beast.util.TreeParser" taxa="@AARS"
IsLabelledNewick="true"
newick='((((((val_1gax_t_therm17A-aa:0.1):100, (gly_2zt5_h_h_sap1A-aa:0.1, gly_d1atib_therm2A-aa:0.1, gly_d1j5wb_itima3A-aa:0.1):100):100, ((ala_1yfsa__licus19A-aa:0.1, ala_2ztg_a__fulg1A-aa:0.1, ala_2zze_p__hori2A-aa:0.1, ala_3hxv_e__coli2A-aa:0.1):100, (asp_d1b8aa_ensis2A-aa:0.1, asp_d1c0aa__coli1A-aa:0.1, asp_d1efwa_therm2A-aa:0.1, asp_1wydb__odaii1B-aa:0.1, asp_3i7f_e_ytica1A-aa:0.1):100):100):100, (((pro_2i4la__stris20A-aa:0.1, pro_2j3mb__calis19B-aa:0.1, pro_d1hc7a_therm18A-aa:0.1, pro_d1nj1a_therm2A-aa:0.1, pro_d1nj8a_janas1A-aa:0.1, pro_3ial_g__lamb1A-aa:0.1):100, (glu_1j09_t_therm1A-aa:0.1, glu_1nzj_e__coli2A-aa:0.1, glu_2cfo_t_elong3A-aa:0.1, glu_2o5r_t_itima4A-aa:0.1):100):100, ((ser_d1sera_therm20A-aa:0.1, ser_1wleb__aurus19B-aa:0.1, ser_2cjab__rkeri2B-aa:0.1):100, (leu_1wz2_p__hori1A-aa:0.1, leu_2v0c_T_thermophilus:0.1):100):100):100):100, ((((arg_1iq0_t_therm19A-aa:0.1, arg_3fnr_c_pyl_j20A-aa:0.1, arg_2zue_p__hori18A-aa:0.1, arg_1f7u_s_cerev19A-aa:0.1):100, (thr_d1evka__coli20A-aa:0.1, thr_d1nyra_ureus19A-aa:0.1, thr_3a32_a_ernix20A-aa:0.1):100):100, ((ile_1ile_t_therm19A-aa:0.1, ile_1qu2_s_ureus2A-aa:0.1):100, (gln_1qtq_e__coli1A-aa:0.1, gln_2hz7_d_radio2A-aa:0.1):100):100):100, (((asn_d1asza_therm1A-aa:0.1, asn_1x54a__oshii1A-aa:0.1, asn_3m4p_e_histo1A-aa:0.1):100, (cys_3c8z_m__smeg17A-aa:0.1, cys_1li5_e__coli1A-aa:0.1):100):100, ((tyr_2cyb_a__fulg20A-aa:0.1, tyr_1h3f_t_therm18A-aa:0.1, tyr_1jil_s_ureus19A-aa:0.1, tyr_1wq4_e__coli20A-aa:0.1, tyr_2cya_a_ernix17A-aa:0.1, tyr_2cyc_p__hori18A-aa:0.1, tyr_2dlc_s_cerev18X-aa:0.1, tyr_2zp1_m_annas19A-aa:0.1):100, (his_1htt_e__coli1A-aa:0.1, his_1wu7a___acid1A-aa:0.1, his_3hri_t_rucei1A-aa:0.1, his_3lc0_t_cruzi2A-aa:0.1, his_d1adjc_therm2A-aa:0.1, his_d1qe0a_aureu3A-aa:0.1):100):100):100):100):100, (((met_1pfv_e__coli1A-aa:0.1, met_1woy_t_therm2A-aa:0.1, met_2csx_a__aeol3A-aa:0.1, met_2x1l_m_matis4A-aa:0.1, met_1rqg_p_byssi1A-aa:0.1):100, (trp_1i6m_b_stear1A-aa:0.1, trp_2el7_t_therm2A-aa:0.1, trp_2g36_t_itima4A-aa:0.1, trp_1r6u_h_h_sap19B-aa:0.1, trp_2ip1_s_cerev20A-aa:0.1):100):100, ((lys_3e9h_b_stear3A-aa:0.1, lys_3g1z_s_urium2A-aa:0.1, lys_d1e1oa__coli1A-aa:0.1, lys_3bju___piens1A:0.1):100, (phe_2alya__therm1A-aa:0.1, phe_2rhq_s_cus_a2A-aa:0.1, phe_3l4g_h_h_sap1A-aa:0.1):100):100):300);'
/>
</run>
</beast>