#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; 10:54 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 1766 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep1766;
        DIMENSIONS NTAX=13;
        TAXLABELS
            Aeropyrum_pernix
            Archeoglobus_fulgidis
            Desulfurococcus_mobilis
            Halobacterium_halobium
            Halobacterium_marismortui
            Methanococcus_jannaschii
            Methanococcus_kandleri
            Pyrobaculum_aerophilum
            Pyrococcus_horikoshii
            Pyrococcus_woesii
            Sulfolobus_solfataricus
            Thermococcus_celer
            Thermoplasma_acidophilum
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M597]

	TITLE 'Archaebacterial EF-1alpha';
	LINK TAXA = TaxaForAnalysisStep1766;
	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         ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         ]
Aeropyrum_pernix              STLVGHLLYRLGYIEEKKLKELEQAKSRGKSFKFAWILDKMKEERERGITIDLTFMKFETKKYVFTIIDAPGHRDFVKNMITGASQADAAILVVSATREHLLLARTMGIEQIIVAVNKMDNYDQKRYEFVFIPVSAWKGDNLPWYPTLVEALDPAKPVDKPLRIPVQNVGRVETGVLRGDKVVFMPPGVVGEVRSIMHAEPGDNIGFAITVGYTPVIHVHTASVSSRIIEIKAKLDQFLKAGDAAIVRFKPLVVEKFSEIPQLGRFAMR
Archeoglobus_fulgidis         STLIGRLLYETGEIPEHIIEKMKEAQEKGKTFEFAWVMDRLKEERERGVTIDVAHRKFQTDKYYITIVDCPGHRDFIKNMITGASQADAAVLVMDVTREHIFLARTLGINQIIVAINKMDNYDQKEYEAAFIPVSAYYGDNVPWYPTLLEAFDPEKLVDKPLRIPIQDVGRVESGVLRGDKVVFEPAGVSGEVKSIMHAYPGDNIGFNITVGYTPVVHAHTAQIACRFVELQKKIDQFLKTGDAAIVKLEPMVIERVKDIPPMGRFAIR
Desulfurococcus_mobilis       STMTGHILYRLGYFDEKTVKMIEESKKMGKSFKFAWLLDRMKEERERGVTISLSYMKFETKKYFFTIIDAPGHRDFVKNMITGASQADAAILVVSATREHAILARTMGINQLIVAINKMDPYSEKRYNEIFIPISAWTGENLPWYPTLVEALDPPKPINKPLRIPIQDVGRVETGVLKGDKLVFMPAGLVAEVKTITHAEPGDNIGFNIAVGYTPVIHVHTASVACRITEIIAKIDHFLKQGDIAIVKFKPLVVEKYSDFQGLGRFAMR
Halobacterium_halobium        STMVGRLLYETGSVPEHVIEQHEEAEEEGKGFEFAYVMDNLAEERERGVTIDIAHQEFTTDEYEFTIVDCPGHRDFVKNMITGASQADNAVLVVAATREHVFLSRTLGIDELIVAVNKMDDYDESKYNEVFIATSAFEGDNVPWYPTLLEALNPQPPTDADLRLPIQDVGRIETGVMNGDNVSFQPSDVGGEVKTIMHAEPGDNVGFNITAGYTPVFHAHTAQVACTIESIDKKMDDFIQSGDAAVVTVRPLSLEPSSEIPELGSFAVR
Halobacterium_marismortui     STLVGRLLYETGSVPEHVIEQHEEAEEKGKGFEFAYVMDNLAEERERGVTIDIAHQEFSTDTYDFTIVDCPGHRDFVKNMITGASQADNAVLVVAATQEHVFLARTLGIGELIVAVNKMDDYGESEYKQVFIPVSAFEGDNIGWYEILLEALNPEPPTDAPLRLPIQDVGRVETGILNGDNVSFQPSDVSGEVKTVMHAEPGDNVGFNITEGYTPVFHAHTAQVACTVESIDKKIDDFIQNGDAAVVTVRPLSIEPSSEIPELGSFAIR
Methanococcus_jannaschii      STTVGRLLYDSGAIDPQLLEKLREAQERGKGFEFAYVMDNLKEERERGVTIDVAHKKFETQKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVDVTREHMFLARTLGIKQIAVAINKMDNYSQEEYEKMFIPTASLKGDNVPWYPTLVEALDPEKPTNLPLRIPIQDVGRVETGILRGDKVVFEPAGVSGEVKSIMHAEPGDNIGFNITVGYTPVFHAHTAQVACTFIELLKKLDQFLKTGDAAIVKIKPMVIENVREIPQLGRFAIR
Methanococcus_kandleri        STTVGRLLLDGGAIDPQLIVRLKEAEEKGKGFEFAYVMDGLKEERERGVTIDVAHKKFPTAKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVNVTREHVFLIRTLGVRQLAVAVNKMDNFSEADYNELFVPVASLHGDNVPWYPTIAEVIDPEKPTNLPLRLPIQDVGRVETGIIKGDKVVFEPAGAIGEIKTVMHAEPGDNIGFNLTDGYTPVFHTHTAQIACTFAEIQKKLNDFLKAGDAAIVKLIPMVIESVKEIPQLGRFAIR
Pyrobaculum_aerophilum        STLVGRLLYETGYVDEKALKEIEMAKKIGKDFAFAWILDRFKEERERGVTIEATHVGFETNKLFITIIDLPGHRDFVKNMIVGASQADAALFVISAGREHLFLIRTLGVQQIVVAVNKMDNYDQKRYEQVFIPVSAIKGDNIPWYPTLLEVFDPQRPVDKPLRMPIQDVGRVETGVLKGDRVVIVPPAKVGDVRSITHAQPGDNIGVNIGPGYAPVMHIHTATVPVQITELVSKLDQFIKQGDVAIVKIKPVVAEKFSDFPPLGRFALR
Pyrococcus_horikoshii         STTIGRLLYDTGNIPETIIKKFEEMGEKGKSFKFAWVMDRLKEERERGITIDVAHTKFETPHRYITIIDAPGHRDFVKNMITGASQADAAVLVVAATKEHAFLARTLGIKHIIVTINKMDNYDQKVFEKVVIPTSAWNGDNVPWYPTLIEALDPEKPIDKPLRIPIQDVGRVETGKLKGDVVIFEPASIQGEVKSIMHALPGDNIGFNITVGYSPVLHAHTAQIPVRFEQILAKVDQFIKTGDSAIVVLRPVVLEPVKEIPQLGRFAIR
Pyrococcus_woesii             STTIGRLLYDTGNIPEQIIKKFEEMGEKGKSFKFAWVMDRLREERERGITIDVAHTKFETPHRYITIIDAPGHRDFVKNMITGASQADAAVLVVAATKEHAFLARTLGIKHIIVAINKMDNYNQKRFEEVVIPISAWEGENVPWYPTLIEALDPEKPVDKPLRIPIQDVGRVETGKLRGEVVIFEPASIQGEVKSIMHALPGDNIGFNITVGYSPVLHAHTAQVPVRFEQLLAKLDQFIKTGDAAIVILRPVVLEPVKEIPQLGRFAIR
Sulfolobus_solfataricus       STLVGRLLMDRGFIDEKTVKEAEAAKKLGKSEKFAFLLDRLKEERERGVTINLTFMRFETKKYFFTIIDAPGHRDFVKNMITGASQADAAILVVSATREHIILAKTMGLDQLIVAVNKMDPYDEKRYKEIFVPVVAPSGDNIKWYPTLEEYLDPPKPVDKPLRIPIQDRGRVESGVLKGDKIVFMPAGKVGEVRSITHAEPGDNIGFNLANGYTPVLHVHTASVACRVSELVSKLDQFLKQGDVAIVKFKPLCVEKYNEFPPLGRFAMR
Thermococcus_celer            STTIGRLLFDTANIPENIIKKFEEMGEKGKSFKFAWVMDRLKEERERGITIDVAHTKFETPHRYITIIDAPGHRDFVKNMITGASQADAAVLVVAVTKEHAFLARTLGINNILVAVNKMDNYDEKKFKAVIIPISAWEGDNVPWYPTLIEALDPPKPTDKPLRIPIQDVGRVETGVLRGDVVIFEPASIQGEVKSIMHALPGDNIGFNITVGYTPVLHAHTLQVAVRFEQLLAKLDQFIKTGDSAIVVLRPMVIEPVKEIPQMGRFAIR
Thermoplasma_acidophilum      STLVGRLLYEHGEIPAHIIEEYKEAEQKGKTFEFAWVMDRFKEERERGVTIDLAHRKFETDKYYFTLIDAPGHRDFVKNMITGTSQADAAILVISATREHAFLARTLGVPQMVVAINKMDPYSEKRYNEVFVPISGYKGDNVPWYPTLLQALDPEKPINKPLRIPVEDVGRVETGVLKGDKVIFLPADKQGDVKSIMHAEPGDNIGFNIAPGYKPVFHVHTAQVACRIDEIVKTLNDFIKNGDVAIVKVIPLVIEKVSEIPQLGRFAVL
;
END;

[ The following blocks are output data for analysis step 1766 ]
BEGIN TREES;
      TITLE Tb6542;
      LINK TAXA = TaxaForAnalysisStep1766;
      TREE 'Archaebacterial EF-1alpha' = [&R] (Desulfurococcus_mobilis,Sulfolobus_solfataricus,(Aeropyrum_pernix,(Pyrobaculum_aerophilum,(Thermoplasma_acidophilum,((Archeoglobus_fulgidis,((Halobacterium_marismortui,Halobacterium_halobium),(Methanococcus_kandleri,Methanococcus_jannaschii))),(Thermococcus_celer,(Pyrococcus_woesii,Pyrococcus_horikoshii)))))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4181]


END;