#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; 10:55 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 1770 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep1770;
        DIMENSIONS NTAX=27;
        TAXLABELS
            Acrasis_rosea
            Arabidopsis_thaliana
            Blastocystis_hominis
            Caenorhabditis_elegans
            Cryptosporidium_parvum
            Cyanophora_paradoxa
            Dictyostelium_discoideum
            Dinenympha_exilis
            Entamoeba_histolytica
            Euglena_gracilis
            Giardia_lamblia
            Hexamita_inflata
            Homo_sapiens
            Naegleria_andersoni
            Nicotiana_tabacum
            Physarum_polycephalum
            Phytophthora_capcisi
            Plasmodium_falciparum
            Podospora_anserina
            Porphyra_purpurea
            Schizosaccharomyces_pombe
            Spironucleus_barkhanus
            Stylonychia_lemnae
            Tetrahymena_pyriformis
            Trichomonas_vaginalis
            Trypanosoma_brucei
            oxymonad
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M126]

	TITLE 'Eukaryotic EF-1alpha';
	LINK TAXA = TaxaForAnalysisStep1770;
	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         ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         ]
Acrasis_rosea                 STTTGHLIYKCGGIDKRVIEKFKEAAEIGKSFKYAWVMDKLKAEKERGITIDISLWKFQSAKYDFTIIDAPGHRDFIKNMITGTSQADVAILMIDSTREHALLAQTLGVKQMIVCLNKFDNFSQARYDEIFIPLSGFQGYNMPWYPCLLEALDPKRPTDKPLRLPLQDVGRVETGLLKGMNVTFAPGNKTTEVKSVMHAEPGDNVGFNISNGYSPVLDCHTAHIACKFETIKSLIDKGLKRGDSGIVKLVPMCVESYTEYPPLGRFAVR
Arabidopsis_thaliana          STTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAERDRGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTREHALLAFTLGVKQMICCCNKMDKYSKARYDEIFVPISGFEGDNMDWYPTLLEALDPKRPSDKPLRLPLQDVGRVETGMIKGMVVTFAPTGLTTEVKSVMHALPGDNVGFNIGNGYAPVLDCHTSHIAVKFSEILTKIDKFLKNGDAGMVKMTPMVVETFSEYPPLGRFAVR
Blastocystis_hominis          STTTGHLIYACGGIDKRTIERFEGGQRIGKSFKYAWVLDKMKAERERGITIDISLWKFQTEKYFFTIIDAPGHRDFIKNMITGTSQADVAILIIAATREHALLANTLGVKQMICCVNKMDNYSEARYKEIFIPISGFNGDNMPWYPTLIEALDPKRPVDKPLRLPLQDVGRVETGILKGMTVTFAPVGVTTEVKSVMHALPGDNVGFNIRPGYCPVMDCHTAHIACKFEKIMSEMDDIVKNGKSMMAELVPLCVESFQDYPPLGRFAVR
Caenorhabditis_elegans        STTTGHLIYKCGGIDKRTIEKFKEAQEMGKSFKYAWVLDKLKAERERGITIDIALWKFETAKYYITIIDAPGHRDFIKNMITGTSQADCAVLVVACTREHALLAQTLGVKQLIVACNKMDPFSEARFTEIFVPISGFNGDNMPWFKTLLEALDPQRPTDRPLRLPLQDVGRVETGIIKGMVVTFAPQNVTTEVKSVMHAVPGDNVGFNISNGYTPVLDCHTAHIACKFNELKEKVDKFLKSGDAGIVELIPLCVESFTDYAPLGRFAVR
Cryptosporidium_parvum        STTTGHLIYKLGGIDKRTIEKFKESSEMGKSFKYAWVLDKLKAERERGITIDIALWQFETPKYHYTVIDAPGHRDFIKNMITGTSQADVALLVVPATREHALLAFTLGVRQMIVGINKMDEYKQSRFDEIFVAISGFVGDNMPWYKTLVEALDPKRPTDKPLRLPLQDVGRVETGIIRGMNVTFAPAGVTTEVKSVMHAVPGDNVGFNIKNGYSPVVDCHTAHISCKFQTITAKMDKLIKSGDAALVVMQPLCVEAFTDYPPLGRFAVR
Cyanophora_paradoxa           STTTGHLIYKCGGIDKRTIEKFKEAAEIGKSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTIIDAPGHRDFIKNMITGTSQADCAVLVIPATREHALLAYTLGVKQMIVAVNKMDNYGQPRFEEIFVPISGFNGDNMGWYPTLVEALDPKRPSEKPLRLPLQDVGRVETGVIKGMTVVFAPSAVTTEVKSVMHALPGDNVGFNIGAGYSPVVDCHTAHIACKFSELITKIDKFVKSGDACMARLIPMCVEAFTNYPPLGRFAVR
Dictyostelium_discoideum      STTTGHLIYKCGGIDKRVIEKYKEASEMGKSFKYAWVMDKLKAERERGITIDIALWKFETSKYYFTIIDAPGHRDFIKNMITGTSQADCAVLVIASTREHALLAYTLGVKQMIVAINKMDNYSQARYDEIFVPISGWNGDNMEWYPTLLEALDPKRPHDKPLRIPLQDVGRVETGIIKGMVVTFAPAGLSTEVKSVMHARPGDNVGFNIHAGYSPVLDCHTAHIACKFTEIVDKVDVVLKNGDAAMVELTPMCVESFTEYPPLGRFAVR
Dinenympha_exilis             STTTGHLIYKCGGIDERTIKKFQESEAMGKSFKYAWVLDKLKAERERGITIDIALWKFETNKYYFTIIDAPGHRDFIKNMITGTSQADAAILVVAATREHALLAYTLGVEQMIVCVNKMDNWAESRYNEIMIPISGFNGDNMPWYPILFDALDPKRPSDKPLRLPIQDVGRVETGILTGQVITIAPCMITTEVKSVMHAVPGDNVGFNIQNGYTPVLDCHTSHIACKFKEIQSKIDKFIKTGDSAIVEMQPMVVETFVEYPPLGRFAVR
Entamoeba_histolytica         STTTGHLIYKCGGIDQRTIEKFKESAEMGKSFKYAWVLDNLKAERERGITIDISLWKFETSKYYFTIIDAPGHRDFIKNMITGTSQADVAILIVAATREHILLSYTLGVKQMIVGVNKMDQYKQERYEEIFVPISGFQGDNMPWYPTLIGALDPERPVDKPLRLPLQDVGRVETGILKGTIVQFAPSGVSSECKSIMHAIPGDNVGFNIRKGYTPVLDCHTSHIACKFEELLSKIDEYIKNGDSALVKIVPLCVEEFAKFPPLGRFAVR
Euglena_gracilis              STTTGHLIYKCGGIDKRTIEKFKEASEMGKSFKYAWVLDKLKAERERCITIDIALWKFETAKSVFTIIDAPGHRDFIKNMITGTSQADAAVLVIDSTREHALLAYTLGVKQMIVATNKFDKYSQARYEEIFIPISGWNGDNMGWYLTLIGALDPKRPSDKPLRLPLQDVGRVETGVLKGDVVTFAPNNLTTEVKSVMHAVPGDNVGFNIGNGYAPVLDCHTCHIACKFATIQTKIDKFIKSGDAAIVLMKPMCVESFTDYPPLG-VSCG
Giardia_lamblia               STLTGHLIYKCGGIDQRTIDEYKRATEMGKSFKYAWVLDQLKDERERGITINIALWKFETKKYIVTIIDAPGHRDFIKNMITGTSQADVAILVVAATREHATLANTLGIKTMIICVNKMDKYSKERYDEIYIPTSGWTGDNIPWYPCLIDAIDPKRPTDKPLRLPIQDVGRVETGELAGMKVVFAPTSQVSEVKSVMHAGPGDNVGFNIQPGYTPVIDCHTAHIACQFQLFLQKLDPDAGRGDCIIVKMVPLCCETFNDYAPLGPFAVR
Hexamita_inflata              STLTGHLIYKCGGIDQRTLEDYKKANEIGKSFKYAWVLDQLKDERERGITINIALWKFETKKFIVTIIDAPGHRDFIKNMITGTSQADVAILVVAATREHATLANTLGIKTMIVAVNKMDNYSEARYTEIFVPLSGWTGDNIPWYKCLIECIDPKRPNDKPLRLPIQDVGRVESGELIGMMVVFAPAGEKTEVKSVMHAGPGDNVGFNINPGYTPVLDCHTSHLAWKFDKFLAKLNTEAVRGECVLMQIVPLCVESFEQYPALGRFAVR
Homo_sapiens                  STTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAERERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAATREHALLAYTLGVKQLIVGVNKMDPYSQKRYEEIFVPISGWNGDNMPWFTTLLEALDPTRPTDKPLRLPLQDVGRVETGVLKGMVVTFAPVNVTTEVKSVMHALPGDNVGFNISAGYAPVLDCHTAHIACKFAELKEKIDKFLKSGDAAIVDMVPMCVESFSDYPPLGRFAVR
Naegleria_andersoni           STTTGHLIYKCGGIDKRVIEKFKEAAEMGKSFKYAWVLDKLKAERERGITIDIALWKFESKKYVFTIIDAPGHRDFIKNMITGTSQADVAILVVDSTREHALLAYTLGIKQMIVCMNKFDSYKEDRYNEIFVPISGWTGDNMPWYPCLLDALDPVRPTDKPLRLPFQDVGRVETGKLKGMMIHFAPGQADTEVKSVMHAGPGDNVGFNIRAGYTPVLDCHTSHIACKFDKLIDKIDEKIKKGDSAIVQVIPMCVEGFTEYPPLGRFAVR
Nicotiana_tabacum             STTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAERERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTREHALLAFTLGVKQMICCCNKMDKYSKARYDEIFVPISGFEGDNMDWYPTLLEALDPKRPSDKPLRLPLQDVGRVETGVLKGMVVTFGPTGLTTEVKSVMHALPGDNVGFNIGNGYAPVLDCHTSHIAVKFAEILTKIDKFLKNGDAGMVKMIPMVVETFSEYPPLGRFAVR
Physarum_polycephalum         STTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKSERERGITIDIALWKFETAKYYITIIDAPGHRDFIKNMITGTSQADAAVLVIASTREHALLAYTLGVKQMIVAINKMDNWSQARYDEIFVPISGWNGDNMPWYPTLLEALDPKRPTDKPLRVPLQDVGRVETGILKGMIVTFAPANLSTEVKSVMHAVPGDNVGFNIHAGYAPVLDCHTAHIACKFTEILSKVDKNIKNGDAAIVKLTPMCVESFTDFPPLGRFAVR
Phytophthora_capcisi          STTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDNLKAERERGITIDIALWKFESPKYFFTVIDAPGHRDFIKNMITGTSQADCAILVVASTREHALLAFTLGVKQMVVAINKMDMYGQARYEEIFVPISGWEGDNMPWYPFLLEALDPKRPSDKPLRLPLQDVGRVETGVIKGMVATFGPVGLSTEVKSVMHAVPGDNVGFNIGNGYSPVLDCHTAHVACKFKEITEKMDKFVKSGDACMVILEPMTVESFQEYPPLGRFAVR
Plasmodium_falciparum         STTTGHIIYKLGGIDRRTIEKFKESAEMGKSFKYAWVLDKLKAERERGITIDIALWKFETPRYFFTVIDAPGHKDFIKNMITGTSQADVALLVVPATKEHALLAFTLGVKQIVVGVNKMDKYSEDRYEEIFIPISGFEGDNLPWYRTLIEALDPKRPYDKPLRIPLQGVGRVETGILKGMVLNFAPSAVVSECKSVMHARPGDNIGFNIKNGYSPVLDCHTAHISCKFLNIDSKIDKSIKSGDSALVSLEPMVVETFTEYPPLGRFAIR
Podospora_anserina            STTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAERERGITIDIALWKFETPKYYVTVIDAPGHRDFIKNMITGTSQADCAILIIAATREHALLAYTLGVKQLIVAINKMDKWSEARFNEIFVPISGFNGDNMPWYKTLLEAIDPKRPTDKPLRLPLQDVGRIETGILKGMVVTFAPSNVTTEVKSVMHGVPGDNVGFNVGAGYAPVLDCHTAHIACKFSELLQKIDKFIKSGDAAIVKMVPMCVEAFTEYPPLGRFAVR
Porphyra_purpurea             STTTGHLIYKCGGIDKRAIEKFKEAAEMGKSFKYAWVLDKLKAERERGITIDIALWKFETDKYNFTIIDAPGHRDFIKNMITGTSQADLAILVIASTREHALLAYTLGVKQMIVACNKMDNWSKERYEEVKVPTSGWTGENLKWYPCLLEALDPKRPVDKPLRLPLQDVGRVETGVIKGMVVTFAPSGLSTEVKSVMHAGPGDNVGFNIHAGYAPVLDCHTAHIACKFSELILKMDKMIKSGDAAMVKMVPMCVEAFTSYPPLGRFAVR
Schizosaccharomyces_pombe     STTTGHLIYKCGGIDKRTIEKFKEATELGKSFKYAWVLDKLKAERERGITIDIALWKFETPKYNVTVIDAPGHRDFIKNMITGTSQADCAVLIIGGTREHALRAYTLGVKQLIVAVNKMDGWSQARFEEIFVPVSGFQGDNMPWYKTLLEAIDPARPTDKPLRLPLQDVGRVETGVIKGMIVTFAPAGVTTEVKSVMHGLPGDNVGFNISAGYSPVLDCHTAHIACKFAELIEKIDKFVKSGDACIAKMVPMCVEAFTDYAPLGRFAVR
Spironucleus_barkhanus        STLTGHLIYKCGGIDQRTLDEYKRANEMGKSFKYAWVLDQLKDERERGITINIALWKFETKKFTVTIIDAPGHRDFIKNMITGTSQADVAILVIASTREHATLAHTLGIKTLIVCVNKMDNYSEARYKEIFIPTSGWTGDSIPWYPCLIDAIDPKRPTDKPLRLPIQDVGRVESGLLINMTVVFAPSTTTAEVKSVMHAGPGDNVGFNIQPGYSPVIDCHTAHIACKFDAFLQKLNTEASRGECIVVRMVPLSCESFNDYAALGRFAVR
Stylonychia_lemnae            STSTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAERERGITIDIALWNFETAKSVFTIIDAPGHRDFIKNMITGTSQADAAILIIASTREHALLAFTMGVKQMIVAVNKMDNWDQGRFIEIFIPISGWHGDNMPWFSTLIDALDPKRPKDKPLRLPLQDVGRVETGLLKGMVLTFAPMNITTECKSVMHAEPGDNVGFTIQKGYAPVLDCHTAHIACKFDEIESKVDKFIKSGEAALVRMVPMCVEAFNQYPPLGRFAVR
Tetrahymena_pyriformis        STTTGHLIYKCGGIDKRVIEKFKESAEQGKSFKYAWVLDKLKAERERGITIDISLWKFETAKYHFTIIDAPGHRDFIKNMITGTSQADVAILMIASTREHALLAFTLGVKQMIVCLNKMDNFSEERYQEIFIPISGFNGDNMPWYPILVEALDPKRPVDKPLRLPLQDVGRVETGVIKGMSIQFAPNKVIAECKSVMHAVPGDNVGFNIQAGYTPVLDCHTAHIACKFETIHDKIDKFIKNGDAALVTLIALCVEVFQEYPPLGRYAVR
Trichomonas_vaginalis         STTTGHLIYKCGGLDKRKLAAIKEAEQLGKSFKYAFVMDSLKAERERGITIDISLWKFEGQKFSFTIIDAPGHRDFIKNMITGTSQADAAILVIDSTREHALLAFTLGIKQVIVAVNKMDNYNKARFDEIFVPISGWAGDNMPWYPYLLEALDPKRPFDKPLRLPLQDVGRVESGTMKGMIVNFAPSTVTAEVKSIMHALPGDNIGFNIHAGYQPVFDCHTAHIACKFDKLIQRIDEYIQKDDAAIVEVVPLVVESFQEYPPLGRFAIR
Trypanosoma_brucei            STATGHLIYKCGGIDKRTIEKFKEAADIGKSFKYAWVLDKLKAERERGITIDIALWKFESPKSVFTIIDAPGHRDFIKNMITGTSQADAAILIIASTREHALLAFTLGVKQMVVCCNKMDNYGQERYDEIFVPISGWQGDNMPWYPTLLEALDPVRPSDKPLRLPLQTCGRVETGVMKGDVVTFAPANVTTEVKSIMHATPGDNVGFNIGNGYAPVLDCHTSHIACKFAEIESKIDKSIKSGDAAIVRMVPMCVEVFNDYAPLGRFAVR
oxymonad                      STTTRHLIYKCGGIDQRTLDRFKESEAMGKSFKYAWVLDKLKAERERGITIDIALWKFETGKYYFTIIDAPGHRDFIKNMITGTSQADGAILVVAATREHALLAYTLGVRQMIVCVNKMDNWAESRYNEVMIPISGFNGDNMPWYPVLFEALDPKRPSEKPLRLPIQDVGRVETGILTGQVITIAPCMITTEVKSVMHAVPGDNVGFNIQNGYTPVLDCHTSHIACKFKEIQSKIDKSIKSGDSAFVEMQPMVVETFVEYPPLGRFAVR
;
END;

[ The following blocks are output data for analysis step 1770 ]
BEGIN TREES;
      TITLE Tb6546;
      LINK TAXA = TaxaForAnalysisStep1770;
      TREE EukEF = [&R] (Homo_sapiens,Caenorhabditis_elegans,((Cyanophora_paradoxa,((Phytophthora_capcisi,(Nicotiana_tabacum,Arabidopsis_thaliana)),((Porphyra_purpurea,(Dictyostelium_discoideum,Physarum_polycephalum)),((((oxymonad,Dinenympha_exilis),(Cryptosporidium_parvum,Plasmodium_falciparum)),((Tetrahymena_pyriformis,Entamoeba_histolytica),(Acrasis_rosea,(Blastocystis_hominis,(Trichomonas_vaginalis,(Naegleria_andersoni,(Hexamita_inflata,(Spironucleus_barkhanus,Giardia_lamblia)))))))),(Euglena_gracilis,(Stylonychia_lemnae,Trypanosoma_brucei)))))),(Podospora_anserina,Schizosaccharomyces_pombe)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4185]


END;