#NEXUS
[!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file.


Generated on September 19, 2025; 10:53 GMT

TreeBASE (cc) 1994-2008

Study reference:
Susko E., Field C., Blouin C., & Roger A. 2003. Estimation of Rates-Across-Sites
Distributions in Phylogenetic Substitution Models. Systematic Biology, 52(5): 594-603.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S1019]

[ The following blocks are input data for analysis step 1775 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep1775;
        DIMENSIONS NTAX=17;
        TAXLABELS
            Arabidopsis_thaliana
            Caenorhabditis_elegans
            Candida_albicans
            Dictyostelium_discoideum
            Drosophila_melanogaster
            Euplotes_octocarinatus
            Giardia_lamblia
            Homo_sapiens
            Neurospora_crassa
            Nicotiana_tabacum
            Oxytricha_trifallax
            Plamodium_falciparum
            Saccharomyces_cerevisiae
            Schizosaccharomyces_pombe
            Trichomonas_vaginalis
            Trypanosoma_brucei
            Yarrowia_lipolytica
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M608]

	TITLE Eukaryotic_eRF3;
	LINK TAXA = TaxaForAnalysisStep1775;
	DIMENSIONS NCHAR=269;
	FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -;

MATRIX
[                                     10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         ]
Arabidopsis_thaliana          STIGGQILFLSGQVDDRQIQKYKEAKDKSRSWYMAYIMDTNEEERLKGKTVEVGRAHFETESTRFTILDAPGHKSYVPNMISGASQADIGVLVISATREHVQLAKTLGVSKLIVVVNKMDNWSKERYDEIFLPISGLMGKNMPWWPSFFEVLDPPRDPNGPFRMPIIDKGKVESGSIRGDSLVVMPNKEQVKVVAICDAGPGENLRVRFTAGYKAILHIHAVVEECEIIELKSQIDLFVKNGAAVVCRIQSICIEKFSDFPQLGRFTLR
Caenorhabditis_elegans        STIGGQLMFLTGMVDKRTLEKYREAKEKGRSWYLSWCMDTNDEEREKGKTVEVGRAYFETEKRHFTILDAPGHKSFVPNMIVGANQADLAVLVISATREHSMLVKTAGVKHLVILVNKMDKWEEERFKEIYVPCSGLTGAFINWYPCFIEFIDYKRDFNGPVRCTVAEKGKMESGCVQGDTLVVMPNKQPVQVLQIADVVAGDNIKFKIASGYSCVLHIQSAVEEVTVKGVIATIDKFVKQDEKCIMRLEPFVLEPFKEYPYLGRFTLR
Candida_albicans              STMGGNILYLTGSVDKRTVEKYREAKDAGRGWYLSWVMDTNKEERNDGKTIEVGKAYFETDKRRYTILDAPGHKMYVSEMIGGASQADVGILVISATREHALLAKTQGVNKIIVVVNKMDGWSKERYQECYMPVSGYTGAGLPWYPSLLEYLDMNRKINGPFMMPVSGKGKIESGHVKGTNLIMMPNKTPIEVLTINEAFSGEQVRLKLSNGFSCVMHLHTAIEEVKFIELKHKLEAFAKKGMKIIAILELVCAETYKDYPQLGRFTLR
Dictyostelium_discoideum      STLSGSIMVLTGQVDPHTLAKYREAKENHRGWIYAYIMDTNEEERTKGKTVEVGRAHFETTKKRYTILDAPGHRLYVPNMIIGAAQADVGILVISSTIEHARLAKMIGIKYLVVFVNKMDKWSKARYDEIFVPGSGYGTLNVDWYPSLIGTLDMERNEGGALRIPITTSGKVESGTISGQSIHIMPGKTKVEVISLGDARPGENITIAFTPSFSAIFHAHTAVEDVTVKSLIATIDTFCKVGDAVKCRLVAVCLEEFTTNPQLARFTIR
Drosophila_melanogaster       STIGGQIMSLTGMVHKRTLEKYREAREKSRSWYLSWGLDTNQEERDKGKTVGVGRAFFETDRKHFTILDAPGHKSFVPNMIGGAAQADLAVLVISATREHAMLAKTAGVKHLVVLVNKMDNWDQTRYNECFMPCSGLSGTGLPWYPAFIPFIDLNRKSDGPFIMPIVDKGKVESGTARGQNLLVMPNRTQVAVDQLSDVGPGENVKIKICAGYSAVMHIHCAAEEVTVKALICLVDRFVKQDQVAIMRIEMICLEQFKLFPQMGRFTLR
Euplotes_octocarinatus        STICGNLMFMTGMVDERTTEKFQEAKEKNRSWWLAYVMDINDDEKSKGKTVEVGRATMETPTKRYTIFDAPGHKNYVPDMIMGAAMADVAALVISATREHAQLARSLGVSKLVVVVNKMDQWNEARYNDIFIPISGLNGQNITWYPTLIEILDPKRNADGPLRVPVLDKGKVESGVIKGSKLAVMPNNLKCQVVGINCANPGENIQIKITPGYKSMMHLHTISDEIVIAG-VYELDKYCKSGSKVIVKISPVCLEKYEFIEHMGRFTLR
Giardia_lamblia               STISGHLVSDLGKLDKRQLEKLQQAKALNRSWKYAFAMDTSEEEREKGKTVECARESFLTPNGRITIIDAPGHKGFVHNMISGAAQADTAILVISATSEHALLAYVNGIKQIVCLINKMDEYCKKRYDSIFLPISGFTGENLEWYPSFLDLLDPKRDTKSPLCACVSGHVKVEQGKMSGDTVLCLPENDILDIEGEEEAKAGDNVRIKITSGYSCVAHINLQQVGCQIRAILADLDYIVSTEPLKVRRPTPVCVQSTPGHEALGRIILR
Homo_sapiens                  STIGGQIMYLTGMVDKRTLEKYREAKEKNRTWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISATREHAMLAKTAGVKHLIVLINKMDNWSNERYEECFMPCSGLTGANLPWYLPFIPYLDFNRSVDGPIRLPIVDKGKLESGSICGQQLVMMPNKHNVEVLGISDVAPGENLKIRICPGYNAVLHIHTCIEEVEITALICLVDRFVKQDQVCIARLRTICLETFKDFPQMGRFTLR
Neurospora_crassa             STLGGAILYVTGMVDQRTLDKYREAKDMGRTWYLSWALDLTNEERAKGKTVEVGRGFFETDKRKYSILDAPGHKTYVPNMIGGASQADVGILVISATREHAMLAKTQGVNKLVVVINKMDNWSEERYKECFMPVAAQQTMGIPWYPSLLEYLDLERKVNAPFMMAVSGKGKIEAGVIKGMSLIMMPNKQSIEISAVGEAQCGEQVRLRLTAGFNCVLHVHAAIEEVTFAALLHKLQSHAKKGDSIIARLESVCVERFEDYPQMGRFTLR
Nicotiana_tabacum             STIGGQILLLSGQVDDRTIQKYREAKDKNRSWYMAYIMDTNEEERVKGITVEVGRAHFETDTTRFTILDAPGHKSYVPNMISGRSQADIGLLVISATREHVQLAKTLGVTKFLVVVNKMDNWSKERYDEIFLPISGLLGSNLPWWPCLFETLDPPRDPNGPLRMPIIDKGKIESGSIHGDNLLIIPNKAAVKVLAICDVGPGENVRVRFTAGYKAVLHIHSVVEECEIVELMQQIDLFVKNGAIVLCRVQLICVEKFSDFAQLGRFTLR
Oxytricha_trifallax           STISGNLMYLMGAVDQRTIQKYEEAKEKNRSWWLAYVMDVSEEEKAKGKTVEVGRANIETPKKRWTIFDAPGHKNYVPNMIMGAALADFGALVISATREHIQLAKSLGISKIVVAVNKMDKWSKDRYTEIFVPISGLNGDNLNWYPTLLEILDPQRDPEGPLRIPVLDKGKVESGTVKGDQLAVMPTNLLAQVQTINSAKPGENVQLRLSKGYQFILHIHTVAEEASIIS-SVEKNQFVQSYAKAVCRIQPIPLEKFEFLPQMGRFTMR
Plamodium_falciparum          STACGNILYILGYVDDRTIEKYREAKEKSRSWFLAFIMDINEEERQKGKTVEVGRAHFETKDRRFTILDAPGHKNFIPNMISGAAQADIGVLIISATREHTLLARTLGINQLIVAINKMDNWSESRYEEIFVPISGLTGQNLSWYPTLFNILNPPWDENGPLRIPLLEGGKIESGTLYNMNCTLMPNKVKVKVMNVLEAKPGENVRVRITAGYFCIFHAHTACEEIQFVEMLEVIDKFIKSDCIVTAHFLPVCVEVYDNLPQLGRFTLR
Saccharomyces_cerevisiae      STMGGNLLYLTGSVDKRTIEKYREAKDAGRGWYLSWVMDTNKEERNDGKTIEVGKAYFETEKRRYTILDAPGHKMYVSEMIGGASQADVGVLVISATREHALLAKTQGVNKMVVVVNKMDNWSKERYDQCFMPVSGYSGANLPWYPTLLEYLDVDRHINAPFMLPIAAKGKIESGHIKGQSTLLMPNKTAVEIQNINEAMCGEQVKLRIAAGFSCVMHVHTAIEEVHIVKLLHKLEAFAKKGMKVIAVLEPVCVETYQDYPQLGRFTLR
Schizosaccharomyces_pombe     STLGGNILFLTGMVDKRTMEKIREAKEAGKSWYLSWALDSTSEEREKGKTVEVGRAYFETEHRRFSLLDAPGHKGYVTNMINGASQADIGVLVISATREHAVLARTQGINHLVVVINKMDQWSEERYKECYMPVSAYTGQNVPWYPSLLEYLDLERKVNAPFIMPIASKGKIEAGSIKNSNVLVMPINQTLEVTAIDESICGDQVRLRLTTGYSCVMHIHTAVEGVSFAKLLHKLDMFATKGMKIIAELEPVCMERFEDYQYMGRFTLR
Trichomonas_vaginalis         STLCGHVLYQAGCVDQRTIEQYAESAKEGRSWYFSWVMDLSKEERSKGKTEEVGVAHFETAQNKYTILDAPGHRSYVPQMIGGAVQADVAVLVISATSEHLLIARTAGVREIIIVVNKMDKWSKERFDQIYIPIAALTGFNLPWYPTLFEKLDPVRNETDSFRLPVIDRGKLEKGVIKGDQVIVMPSRKLGTISSIVDAVPGDNIRVAITAGYEAMCHIHTETVPVSVEKL--RTLRFIKRGCLAEVILKPICVEVAKDFPQLGRFIIR
Trypanosoma_brucei            STISGHLLMEKGLVDQREMEKLREAEVHHRGWEYAYVMDVSEDERTKGITRETGAAYVETEKRRITVLDAPGHKAFVPSMIGGATQADVCVLVISSTREHAMLVRTCGVKQMICVINKMDNWSKERYDAIFIPIAGLTGDNLPWYPTMMSFIDPETKSENVLCIPLVGSGKVESGSVAGEKIQILPSKQEAVVEGIIECYPGDNVHLRICAGSRVMLHAHAAQEEVSFHKLLAKVDTHVKAGDVVIARMEALVLEPHKDFDKMGRFMLR
Yarrowia_lipolytica           STLGGQILYLTGTVNKRTIEKMKEAADAGRGWYLSWVMDINKEERAEGKTVEVGRSYFETEKRRYTLLDAPGHKMYVPSMIGGAAQADAGILVISATREHAMLAKTQGINKLVIAINKMDNWSKERYDECFMPVSGFTGANVPWYPSLLELLDLERNLTGPFMLPISNKGKIEVGQVKGDNLVVMPSKVPVEVTTLKEASVGEQIRLKLSTGFSCVMHIHTAAEEVTFTALLHKLEAFAKKGMKIIARLEPVCMDEFSKTPQLGRFTLR
;
END;

[ The following blocks are output data for analysis step 1775 ]
BEGIN TREES;
      TITLE Tb6551;
      LINK TAXA = TaxaForAnalysisStep1775;
      TREE eRF3 = [&R] (Drosophila_melanogaster,Homo_sapiens,(Caenorhabditis_elegans,(((Yarrowia_lipolytica,(Candida_albicans,Saccharomyces_cerevisiae)),(Schizosaccharomyces_pombe,Neurospora_crassa)),((Dictyostelium_discoideum,((Plamodium_falciparum,(Oxytricha_trifallax,Euplotes_octocarinatus)),(Nicotiana_tabacum,Arabidopsis_thaliana))),(Trichomonas_vaginalis,(Trypanosoma_brucei,Giardia_lamblia))))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4190]


END;