#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 1771 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep1771;
        DIMENSIONS NTAX=17;
        TAXLABELS
            Agrotis_ipsilon
            Aspergillus_terreus_1
            Blattella_germanica
            Candida_utilis
            Cricetulus_griseus
            Dendroctonus_jeffreyi
            Drosophila_melanogaster
            Gibberella_fujikuroi
            Homo_sapiens
            Ips_paraconfusus
            Oryctolagus_cuniculus
            Phycomyces_blakesleeanus
            Rattus_norvegicus
            Saccharomyces_cerervisiae_1
            Schizosaccharomyces_pombe_1
            Strongylocentrotus_purpuratus
            Xenopus_laevis
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M602]

	TITLE 'Eukaryotic HMG-CoA';
	LINK TAXA = TaxaForAnalysisStep1771;
	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 ]
[                                          .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Agrotis_ipsilon                   ENVIGYVGVPVGYAGPLVVDGKPYMIPMATTEGALVASTNRGAKAIVTSVVEDVGMTRAPAICRQWIAVIKEAFDSTSRFLQEIHIGVYLRFRATTGDAMGMNMVSKGAENALKLLMEVISLSGNYRVVCETTITSDSLRTDAKTLARCNKISALAGSINAANMVTAIYIATGQDPAQNVTSTNMELYVTCTMPLEVGTVGGGILTGQGACLDILGVSARLICATVLAGELSLMAALVNSDLVKSHMRHNR
Aspergillus_terreus_1             ENVVGYLPLPLGVAGPMVIDGQALFIPMATTEGVLVASASRGCKAIATTMLKGDGMTRGPCLAQRWVEVLAAAFNATSRFLQTLTVAQYIRFRTTTGDAMGMNMISKGVEKALEAMMHTVTLSGNFSVIAEATIPAETVRTDVDALVELNTASAMAGSLFASNLVQAVFLATGQDPAQNVEITTMKLHIAVSMPMEVGTIGGGILEAQGAMLDLLGVARRIVAAAVLAGELSTCAALAAGHLVNAHMQHNR
Blattella_germanica               ENVIGYMPVPVGVAGPLNLDGRLVHVPLATTEGCLVASTNRGMRALVTSRIVADGMTRGPVVAMLWMEQIKKNFDSTSRFLSKIHIRVFIRFIATTGDAMGMNMLSKGTEVALAYVMEILSLSGNFSVVCEAIVPADIIKTSVQALMDVNITSAVAGSIFAANIVTAIFIATGQDPAQNVGMTLMELYVSCTMPIEIGTIGGGVLPPQAACLDMLGVANTIVCGTVLAGELSLMSALAAGHLVKSHMRHNR
Candida_utilis                    ENVIGYMPLPVGVAGPLIIDGKPYHIPMATTEGCLVASAMRGCKAIVTTVLTKDGMTRGPCVCKLWLEEMKKAFNSTSRFLQHLQTALFIRFRTVTGDAMGMNMISKGVEYALKQMMMVVSVSGNYSVVAEASIPKDAVVSSVKAVVDVNVNSAMAGSVFAANMVTAVYLALGQDPAQNVEITLMTLKVSVSMPIEVGTIGGGILDPQGSMLELLGVARQIVASIVLSGELSLVSALAAGHLVQSHMQHNR
Cricetulus_griseus                ENVIGYMPIPVGVAGPLCLDGKEYQVPMATTEGCLVASTNRGCRAIASSRVLADGMTRGPVVVKAWLAVIKDAFDSTSRFLQKLHVTMYIRFQSKTGDAMGMNMISKGTEKALLKLMQILAVSGNYTVVCEAVIPAKVVRTTTEAMIDVNINSAMAGSIYAANIVTAIYIACGQDAAQNVGITLMELYISCTMPIEIGTVGGGNLLPQQACLQMLGVARQIVCGTVMAGELSLMAALAAGHLVRSHMVHNR
Dendroctonus_jeffreyi             ENVIGYMPIPVGYAGPLLLDGRELYIPMATTEGCLVASTNRGCRALVTSSVVADGMTRGPVVAMQWIKKIKEQFDSSSRFLQRLTLKIFIRFIATTGDAMGMNMLSKGTEYSLKLVMEILSLSGNFSVVCEAIVPAKIISTNVHALVDVNNISAVAGSIFAANIVTAIFLATGQDPAQNVSMTLMELYISCTMPIEIGTIGGGILPAQSACLDILGVACQIVCGTVLAGELSLMSALTAGHLVKSHLRHNR
Drosophila_melanogaster           ENVLGYVPIPVGYAGPLLLDGETYYVPMATTEGALVASTNRGCKALVRSVVEDVGMTRAPCVAKSWIRVVKTEFDSTSRFLKDCHIAMYIRFVAITGDAMGMNMVSKGAEMALRRIMQIISLSGNFRVVTECTISAATLRTDAKTLVECNKLSAMAGSINAANMVTAVFLATGQDPAQNVTSTAMELYMTCTMPLEVGTVGGGGLPGQSACLEMLGVAKKIVCATVMAGELSLMAALVNSDLVKSHMRHNR
Gibberella_fujikuroi              ENVIGYMPLPVGVAGPLVIDGQSYFIPMATTEGVLVASASRGCKAIAITVLTADGMTRGPCVAKLWLDMMKKAFNSTSRFLQSMKTALYIRFKTTTGDAMGMNMISKGVEHALSVMMQIISVSGNYGVVAEAIIPGEVVRSDVDSLVELNVASAMAGSVFAANIVAAIFLATGQDPAQVVEITIMKLQISVSMPLEVGTLGGGILEPQGAMLDILGVARRIIGAAVLAGELSLCSALAAGHLVRAHMQHNR
Homo_sapiens                      ENVIGYMPIPVGVAGPLCLDEKEFQVPMATTEGCLVASTNRGCRAIASSRVLADGMTRGPVVVKAWLAVIKEAFDSTSRFLQKLHTSIYIRFQSRSGDAMGMNMISKGTEKALSKLMQILAVSGNYSVVCEAVIPAKVVRTTTEAMIEVNINSAMAGSIYAANIVTAIYIACGQDAAQNVGITLMELYISCTMPIEIGTVGGGNLLPQQACLQMLGVARQIVCGTVMAGELSLMAALAAGHLVKSHMIHNR
Ips_paraconfusus                  ENVIGYMPIPVGYAGPLVLDGKEIYVPMATTEGCLVASTNRGCRALVTSRIVADGMTRGPVVAMQWIDGIKEQFDSSSRFLQRVTMKIFIRFVATTGDAMGMNMLSKGTEYSLKFVMEILSLSGNFSVVCEAIVPAKIVATNVHALVDVNNSSAVAGSIFAANIVTAIFLATGQDPAQNVGMTLMELYISCTMPIEIGTIGGGILPPQGTCLEMLGVASQIVGATVLAGELSLMSALAAGHLVRSHLRHNR
Oryctolagus_cuniculus             ENVIGYMPIPVGVVGPLCLDGKEFQVPMATTEGCLVASTNRGCRAIASSRVLADGMTRGPVVVKAWLAVIKEAFDSTSRFLQKLHISMYIRFQSRTGDAMGMNMISKGTEKALSKLMQILAVSGNYTVVCEAVIPAKVVRTTTEAMIDVNINSAMAGSIYAANYVTAIYIACGQDAAQNVGITLMELYISCTMPIEIGTVGGGNLLPQQACLQMLGVARQIVCGTVMAGELSLMAALAAGHLVKSHMIHNR
Phycomyces_blakesleeanus          ENVIGYMPIPVGVAGPMNIDGDLIHIPMATTEGCLVASTARGCKAIASTIVIADGMTRGPCVCKLWIDIVTNAFNSTSRFLRKLKIALFIRFSTTTGDAMGMNMISKGCEKALSIIMQIISLSGNYSVVTEAVIPGAIVETTVAALVELNISSAMAGSVFAANILTAIYLATGQDPAQNVEITLMKLHISCTMPIEVGTIGGGILPPQQSMLDMLGVAQRIICAAVMAGELSLCAALAAGHLVKAHMAHNR
Rattus_norvegicus                 ENVIGYMPIPVGVAGPLCLDGKEYQVPMATTEGCLVASTNRGCRAIASSRVLADGMSRGPVVVKSWLAVVKEAFDSTSRFLQKLHVTLYIRLQSKTGDAMGMNMISKGTEKALLKLLQILAVSGNYTVVCEAVIPAKVVRTTTEAMVDVNINSAMAGSIYAANIVTAIYIACGQDAAQNVGITLMELYISCTMPIEIGTVGGGNLLPQQACLQMLGVARQIVCGTVMAGELSLMAALAAGHLVRSHMVHNR
Saccharomyces_cerervisiae_1       ENVIGYMPIPVGVIGPLIIDGTSYHIPMATTEGCLVASAMRGCKAIATTVLTKDGMTRGPVVCKIWLNSIKKAFNSTSRFLQHIQTCLFMRFRTTTGDAMGMNMISKGVEYSLKQMMEVVSVSGNYSVVAEATIPGDVVKSDVSALVELNISSAMAGSVFAANLVTALFLALGQDPAQNVEITLMKLRISVSMPIEVGTIGGGVLEPQGAMLDLLGVARQIIACAVLAGELSLCSALAAGHLVQSHMTHNR
Schizosaccharomyces_pombe_1       ENVIGYMPLPLGVAGPLIIDGKPFYIPMATTEGALVASTMRGCKAIAVTVLTRDQMSRGPCVAKIWLEVMKKAFNSTSRFLQHIKTALFIRFCTSTGDAMGMNMISKGVEHALVVMMQVISVSGNYSVIAEAIIPGDAVKTTVEDLVKLNVDSAMAGSVFAANIVTAVYLATGQDPAQNVEITLMDLQLSVSMPIEVGTIGGGVLEPQGAMLDLLGVSRQVVAAAVMAGELSLCSALASGHLVKSHIGLNR
Strongylocentrotus_purpuratus     ENVIGYMPVPVGVAGPLLLDGQEFQVPMATTEGCLVASTNRGCRALIHSVLIGDGMTRGPLVIKQWLAAIKERFESTSRFLKSIQTALFLRFKALTGDAMGMNMISKGTEQALHALIEIMSLSGNYSVVCEATVPAHIVQTSASALVDLNIHSAMAGSIFAANIVTAIYIATGQDAAQNIAMTLMELYLSCTMPIELGTVGGGVLPPQSACLQMMDVASQIVCATVMAGELSLMSALAAGHLVKSHMKHNR
Xenopus_laevis                    ENVIGYMPIPVGVAGPLLLNNKEYQVPMATTEGCLVASTNRGCRAIAKSRVLADGMTRGPVVVKAWLKVIKDAFDSTSRFLGRLQNCVYIRFQSKTGDAMGMNMISKVTEQALARLLHVLAVSGNYSVVCEAIIPAKVVRSSTEALVEVNINSAMAGSIYAANIVTAIYIACGQDAAQNVGITIMELYISCTMPIEIGTVGGGNLAPQQACLQMLGVACQIVCSTVMAGELSLMAALAAGHLVKSHMVHNR
;
END;

[ The following blocks are output data for analysis step 1771 ]
BEGIN TREES;
      TITLE Tb6547;
      LINK TAXA = TaxaForAnalysisStep1771;
      TREE eukHMG = [&R] (Oryctolagus_cuniculus,Homo_sapiens,((Xenopus_laevis,(Strongylocentrotus_purpuratus,((Blattella_germanica,(Ips_paraconfusus,Dendroctonus_jeffreyi)),((Drosophila_melanogaster,Agrotis_ipsilon),(Phycomyces_blakesleeanus,((Saccharomyces_cerervisiae_1,Candida_utilis),(Gibberella_fujikuroi,Aspergillus_terreus_1))))))),(Cricetulus_griseus,Rattus_norvegicus)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4186]


END;