#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; 12:10 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]

BEGIN TAXA;
        TITLE  MDH_ml_distance;
        DIMENSIONS NTAX=14;
        TAXLABELS
            Arabidopsis_thaliana
            Echinococcus_granulosus
            Flaveria_bidentis
            Homo_sapiens
            Medicago_sativa
            Mesembryanthemum_crystallinum
            Mycobacterium_leprae
            Mycobacterium_tuberculosis
            Sorghum_bicolor
            Spinacia_oleracea
            Sus_scrofa
            Thermus_flavus
            Trichomonas_vaginalis
            Zea_mays
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M606]

	TITLE Eukaryotic_cMDH;
	LINK TAXA = MDH_ml_distance;
	DIMENSIONS NCHAR=319;
	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       270       280       290       300       310         ]
[                                          .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         ]
Arabidopsis_thaliana              VRVLVTGAAGQIGYALVPMIARGIMLGADQPVILHMLDIPPAAEALNGVKMELIDAAFPLLKGVVATTDAVEGCTGVNVAVMVGGFPRKEGMERKDVMSKNVSIYKSQAAALEKHAAPNCKVLVVANPANTNALILKEFAPSIPEKNISCLTRLDHNRALGQISERLSVPVSDVKNVIIWGNHSSSQYPDVNHAKVQEKPVRELVKDDAWLDGEFISTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPEGTFVSMGVYSDGSYSVPSGLIYSFPVTCR-NGDWSIVQGLPIDEVSRKKMDLTAEELKEEKDLA
Echinococcus_granulosus           LRVLITGAAGQIAYNLSNMVANGNLFGKDQQIILHLLDIPEAKTVLDGVVMELQDCAFTVLAGIVPTHCLKEAFTDIDVALMVGAMPRKQGMERRDLLSSNVKIFKEQGEALDKYAKKTVKALVVGNPANTNCLIMSKYAPSIPKENFTALTRLDHNRAIYQVAAKAGVPNTCVKNVCIWGNHSNKQFPDLSHAVVTQHPAKELINDEKWVKEVFTPCVQNRGAAVIGLRKLSSAASAAKAIVDQMRDWWFGTKEGEWVSMSVYSTGHYGAPKDIYFSFPVTIK-DGHYKVVDGLSMDEWSRSLFNLSADELVDEREVA
Flaveria_bidentis                 INVAVSGAAGMISNHLLFKLASGEVFGPDQPISLKLLGSERSFAALEGVAMELEDSLYPLLRQVSIGIDPYEIFQDAEWALLIGAKPRGPGMERADLLDINGQIFAEQGKALNAVASPNVKVMVVGNPCNTNALICLKNAPNIPPKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIHGIPVTEVIRDRKWLEDEFTNMVQTRGGVLIKKWGRSSAASTAVSIVDAIRSLVTPTPEGDWFSTGVYTNGPYGIAEDIVFSMPCRSKGDGDYEFVKDVIFDDYLSKKIKKSEDELLAEKKCV
Homo_sapiens                      IRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEDVAFKDLDVAILVGSMPRREGMERKDLLKANVKIFKSQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTANDVKNVIIWGNHSSTQYPDVNHAKVKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGSYGVPDDLLYSFPVVIK-NKTWKFVEGLPINDFSREKMDLTAKELTEEKESA
Medicago_sativa                   VRVLVTGAAGQIGYALVPMIARGVMLGPDQPVILHMLDIAPAAESLNGVKMELVDAAFPLLKGVVATTDVVEACTGVNIAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEKHAAANCKVLVVANPANTNALILKEFAPSIPERNISCLTRLDHNRALGQISERLNVQVSDVKNVIIWGNHSSTQYPDVNHATVNEKPVRQLVSDDAWLNGEFISTVQQRGAAIIKARKLSSALSAASAACDHIRDWVLGTPQGTFVSMGVYSDGSYNVPSGLIYSFPVTCA-NGEWKIVQGLSIDEFSRKKLDLTAEELTEEKNLA
Mesembryanthemum_crystallinum     LRVLVTGAAGQIGYALVPMIARGIMLGANQPVILHMLDIPPAAEALNGVKMELVDAAFPLLKGVVATTDAAEACKGVNVAVMVGGFPRKEGMERKDVMSKNVSIYKAQASALEQHAAPNCKVLVVANPANTNALILKEFAPSIPEKNISCLTRLDHNRALGQISERLNVQVSDVKNVIIWGNHSSTQYPDVNHATVKDKPVRELVADDAWLNGEFITTVQQRGAAIIKARKLSSALSAASSACDHIHDWVLGTPEGTWVSMGVYSDGSYNVPAGIIYSFPVTCK-NGEWTIVQGLPIDDDSRKKMDATAAELVEEKTLA
Mycobacterium_leprae              LKVAVTGAAGQIGYSLLFRLASGSLLGLDRPIELRLLEIEPALKALEGVVMELDDCAFLLLAGVEIGADPNKVFDGVNLALLVGARPRGPGMERGDLLEANGAIFTAQGKALNAVAAADIRVGVTGNPANTNALIAMTNAPDIPRERFSALTRLDHNRAIAQLATKTGSAVTDIRKMTIWGNHSATQYPDVFHAEIGGKNAAEVVGDQAWIEDYFIPTVAKRGAAIIDARGASSAASAASATIDAARDWLLGTPEGNWVSMAVVSDGSYGVPEGLISSFPVTTT-DGDWTIVRGLGIDDFSRGRIDKSTAELADERMAV
Mycobacterium_tuberculosis        LKVAVTGAAGQIGYSLLFRLASGSLLGPDRPIELRLLEIEPALQALEGVVMELDDCAFPLLSGVEIGSDPQKIFDGVSLALLVGARPRGAGMERSDLLEANGAIFTAQGKALNAVAADDVRVGVTGNPANTNALIAMTNAPDIPRERFSALTRLDHNRAISQLAAKTGAAVTDIKKMTIWGNHSATQYPDLFHAEVAGKNAAEVVNDQAWIEDEFIPTVAKRGAAIIDARGASSAASAASATIDAARDWLLGTPADDWVSMAVVSDGSYGVPEGLISSFPVTTK-GGNWTIVSGLEIDEFSRGRIDKSTAELADERSAV
Sorghum_bicolor                   VNIAVSGAAGMISNHLLFKLASGEVFGQDQPIALKLLGSERSFQALEGVAMELEDSLYPLLREVSIGIDPYEVFEDVDWALLIGAKPRGPGMERAALLDINGQIFADQGKALNAVASKNVKVLVVGNPCNTNALICLKNAPDIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIDGRPVKEVIKDTKWLEEEFTITVQKRGGALIQKWGRSSAASTAVSIADAIKSLVTPTPEGDWFSTGVYTTGPYGIAEDIVFSMPCRSKGDGDYELATDVSMDDFLWERIKKSEAELLAEKKCV
Spinacia_oleracea                 ITIAISGAAGTISNHLLFKLASGVVFGPDQPIALKLLGSEKSFHALEGVAMELEDSLYPLLREVSIGIDPYEVFEDAEWALLIGAKPRGPGMERADLLDINGKIYAEQGKALNAVASPNVKVIVVGNPCNTNALICLKNPPNIPAKNFHSLTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFVNAQIGGVPVKEVIKAQKWLEEEFTEKVRKRGGVLIQKWGRSSAASTAVSIVDAINPLITPTPPGDWFPSGVYTNGPYGIAEDLIYSMPCRSKGDGDYELVKDVIFDDYLRKRIKTSEEELLAEKRCT
Sus_scrofa                        IRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKEVGVYEAVKDDSWLKGEFITTVQQRGAAVIKAQKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGSYGVPDDLLYSFPVTIK-DKTWKIVEGLPINDFSREKMDLTAKELAEEKETA
Thermus_flavus                    VRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELV-DMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAK-DGAYRVVEGLEINEFARKRMEITAQELLDEMEQV
Trichomonas_vaginalis             IHILITGAAGQIGYALTFRIAKGDLCG-DRKVVLHLLEIPFGMKALEGCVMELQDCAFPNVAGIVWTDKVEEAFKGVDVAFLVGSFPRKDGMDRSDLLAKNGGIFTVQGKALNDYAKPTVKVLVVGNPANTNCLIAQASAPKLQNKNWCAMTRLDHNRMVGALAAKFGVTPEKIHKVCIWGNHSNTQVPDTTHATVDTVKVADKL-PKEYLEGEFAQMIATRGGAVIKMRGASSAASAANAALTCVKDWLYGTAEGDFVSMAIPVPDPYGIKQGTIFSFPVTVSKDGEVHVVEGLELNDWVKGRLEATEKELIGEKETA
Zea_mays                          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Zea_mays                          MRVLVTGAAGQIGYALVPMIARGVMLGADQPVILHMLDIPPAAEALNGVKMELVDAAFPLLKGVVATTDVVEACTGVNVAVMVGGFPRKEGMERKDVMSKNVSIYKSQASALEAHAAPNCKVLVVANPANTNALILKEFAPSIPEKNVTCLTRLDHNRALGQISERLNVQVSDVKNVIIWGNHSSSQYPDVNHATVKEKPVRELVSDDEWLNGEFITTVQQRGAAIIKARKFSSALSAASSACDHIRDWVLGTPEGTFVSMGVYSDGSYGVPSGLIYSFPVTCS-GGEWKIVQGLPIDEFSRKKMDATAQELTEEKTLA
;
END;