#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; 13:34 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 1767 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep1767;
        DIMENSIONS NTAX=11;
        TAXLABELS
            Aeropyrum_pernix
            Halobacterium_species
            Haloferax_volcanii
            Methanobacterium_thermoautotrophicum
            Methanococcus_jannaschii
            Methanosarcina_mazei
            Pyrobaculum_aerophilum
            Pyrococcus_abyssii
            Pyrococcus_furiosus
            Pyrococcus_horikoshii
            Sulfolobus_solfataricus
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M596]

	TITLE 'Archaebacterial HMG-CoA';
	LINK TAXA = TaxaForAnalysisStep1767;
	DIMENSIONS NCHAR=251;
	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 ]
[                                                 .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Aeropyrum_pernix                         ENPIGAVQVPVGVAGPLRINGDDFYIPLATTEGALVASVNRGAKAIARAKVIKDGMTRAPLLLAMWVEDLRSVVAGVTRHLQHIYPYIWLRLSFSTGDAMGMNMVTISSDRICRYIAKCIALSGNMYVVAEAVIKGEVVKTTPQNINLVNVTSAAAGSHFFANIIAAIFIATGQDAAQVVEYTWTELYISVTLPLEVGTVGGGRLPTQRELLALLGVALKIIASAVLAGELNLLSAIAAGQLARAHELLGR
Halobacterium_species                    ENLTGGAQLPLGVAGPVALSGGEYYLPMATTEGALVASVNRGCSAIANARVTKTGMTRAPVFVAQWADALAAAAESTTSHLTDVTPYVYLRFRYDTKDAMGMNMATIATEAASELVAELVAVSGNLTVTADVTIPQDVVETTPAAIEEANTRSAKAGSLFAANVVAAVFLATGQDAAQVVEITTVELYASVNLALEVGTVGGGTLPTQREALDVLGVADAIIAVGALAGEINLLAALASRRLSAAHADLGR
Haloferax_volcanii                       ENMVGSIQVPMGVAGPVSVDGGEKYLPLATTEGALLASVNRGCSVIATARVLKSGMTRAPVFLVSWTAALKEAAEETTNHLLDVTPYVYLRFRYDTKDAMGMNMATIATEAVCGVVASLVALSGNLSVTADVRIPREVVETTPERGRELNTRSAKAASLFVANVVAAMFLATGQDEAQVVEITTAELYVSVSIALEVGTVGGGKLPTQSEGLDILGVADACIAVGSLAGELSLLSALASRHLSSAHAELGR
Methanobacterium_thermoautotrophicum     ENPIGVVQIPLGVAGPLRVRGEEYYVPLATSEGALVASVNRGCSVIATVRVTGDSMTRAPVILREWIDALREEAESTTRHLVKIDPIVYPRFVYTTGDSMGMNMVTIATERALELLAHVIALSGNLSITAEITVPGEMVETTPEAVVEVNTASAAAGSMFYANIIGAIFLATGQDEAHIVEVTIAELYFAVNLPVPLATVGGGGLETASECLDIMGVVHAIVGGAVLAGELSLMGALAAGHLARAHSELGR
Methanococcus_jannaschii                 ENMIGAIQIPLGFAGPLKINGEEFYIPLATTEGALVASVNRGCSIIATVRVIDDKMTRAPCLVRDWIERIKEVAESTTRHLIKIEPLIYPRFVFKTGDAMGMNMVTIATEKACNFIVKTVAVSGNASIVAEVFLTEKEVNTTSQAIAEVNRLSAISNSMFYANIIGAIFLATGQDEAHIVEITMAELYFSVTLPVPIGTVGGGRVETQKECLEMLGCALKIVGAAVLAGELSLLGALAAGHLGKAHQELGR
Methanosarcina_mazei                     ENMIGAVQIPLGVAGLLKVNGEEYYIPLATTEGALVASVNRGCSVIANVRVFEDEMTRAPVFFYDWVEQMKQAAEKTTRFLLSVKPFVYLRFSYDTKDAMGMNMVTIATDAVMHLIAHPVTLSGNMTVVAEVTIPQEIVKCTPESMFEVNYSSARAGAMFAANIIAAVYLACGQDAAHVVEITSMEIHCSVTLPLPVGTVGGGGLGTQRDCLNILGVSRKIVASAVLAGEISLIGAQAAGHLARAHAQLGR
Pyrobaculum_aerophilum                   ENVIGAVQIPVGVAGPLLVRGDYFYVPLATTEGALVASVNRGAKFVARVKVLKDGMARAPLFLVEWVEELKKVAESTTRFLKDIQHFIWLRLVFSTGDAMGMNMVTIASEAVAKFIAKLIALSGNMTVVAEAVIKKEILEITPEDVHNVNVRSALAHSYFFANIIAAIFIATGQDVAQVVEITSTELYISVFLPLEVGTVGGGGLPTQREALELLGVALKIIAAAVLAGELNLLIALARNELASAHKKLGR
Pyrococcus_abyssii                       ENMIGVVQIPMGVAGPLKINGEEFYIPLATTEGALVASVNRGCSALVVTTILDDKMTRAPLIVAEWVNYLQEAVAKVTRHLRDVKPFIYLRFEFETGDAMGMNMVTIASEEIMKVIVRYLALSGNLTVVAEAIVPREIVETTPELIAEVNYFSAQAGSYFFGNIVGAIFLATGQDEAQITEITIAELYISITMPLEIGTVGGGRVPTQREALSIMGVAKKIVAGAVLAGELSLLAAIAAKHLARAHKMLGR
Pyrococcus_furiosus                      ENMIGVVQIPMGIAGPLKINGEEFYIPLATTEGALVASVNRGCSALVYTTLIDDKMTRAPLLVAEWVDYLQEAVSKVTRHLRGVKPFIYLRFEFETGDAMGMNMVTIASEEIMKVIVKYLALSGNLTIIAEAVVPREIVKTTPELIAEVNYLSAQAGSYFFANIVGAIFLATGQDEAQITEITLAELYISITMPLEIGTVGGGRVPPQREALEIMGVAKKIVAGAVLAGELSLLAAIAAKHLARAHKMLGR
Pyrococcus_horikoshii                    ENMIGVVQIPMGVAGPLKINGEEFYIPLATTEGALVASVNRGCSALVVTTLIDDKMTRAPLIVAKWVDYLQEAVSKVTRHLRGVKPFIYLRFEFETGDAMGMNMVTIASEEIMKVIVRYLALSGNLTVIAEAVVPRKIVETTPELIAEVNYFSAQAGSYFFANIVGAIFLATGQDEAQITEITIAELYISITMPLEIGTVGGGRVPSQREALEIMGVAKKIVAGAVLAGELSLLAAIAAKHLARAHKMLGR
Sulfolobus_solfataricus                  ENVIGAIQIPLGIVGPIRVNGDDFYVPMATTEGALIASVNRGIKAVVRAKVLKDEMTRAPVFFLKFIEKIRNIANSTSHHLKSITPFVWLRFSFETGDAMGMNMVTIAVEKVCEFIADCLAVSGNMTVVAEALIKKDVIRSNAQLIHDINLRTARAGSLFFANIVTAIFIATGQDVAQIVEYTWTELYISVTLPLEVGTVGGGRLPTQKEALSIMGVAKKIIASTVLSGELNLLAALSNKELGKAHAKLGR
;
END;

[ The following blocks are output data for analysis step 1767 ]
BEGIN TREES;
      TITLE Tb6543;
      LINK TAXA = TaxaForAnalysisStep1767;
      TREE ArchaeHMG = [&R] (Halobacterium_species,Haloferax_volcanii,(Methanosarcina_mazei,((Methanobacterium_thermoautotrophicum,Methanococcus_jannaschii),((Pyrococcus_abyssii,(Pyrococcus_furiosus,Pyrococcus_horikoshii)),(Sulfolobus_solfataricus,(Aeropyrum_pernix,Pyrobaculum_aerophilum))))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4182]


END;