#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 June 14, 2024; 6:51 GMT

TreeBASE (cc) 1994-2008

Study reference:
Sant'anna F.H., Lebedinsky A.V., Sokolova T.G., Robb F.T., & Gonzalez J.M. 2015.
Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter
subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase
diversity. BMC Genomics, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S18113]

[ The following blocks are input data for analysis step 16723 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep16723;
        DIMENSIONS NTAX=13;
        TAXLABELS
            'Caldanaerobacter subterraneus pacificus_EEB75482.1'
            'Caldanaerobacter subterraneus tengcongensis_NP_624062.1'
            'Caldanaerobacter subterraneus yonseiensis_ERM91218.1'
            'Caldicellulosiruptor bescii YP_002573898.1'
            'Caldicellulosiruptor hydrothermalis YP_003991814.1'
            'Caldicellulosiruptor kronotskyensis YP_004023322.1'
            Thermoanaerobacter_ethanolicus_EGD52029.1
            Thermoanaerobacter_siderophilus_EIW00263.1
            Thermoanaerobacter_siderophilus_EIW00539.1
            Thermoanaerobacter_thermohydrosulfuricus_EMT39667.1
            'Thermoanaerobacter wiegelii YP_004818845.1'
            'Thermoanaerobacter wiegelii YP_004818850.1'
            'Thermoanaerobacter wiegelii YP_004820398.1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M32949]

	TITLE 11565_alignment;
	LINK TAXA = TaxaForAnalysisStep16723;
	DIMENSIONS NCHAR=386;
	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       320       330       340       350       360       370       380      ]
[                                                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .      ]
'Caldanaerobacter subterraneus pacificus_EEB75482.1'        ---------------------------------MIVQNLRGGIYMVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVILGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAALTPVGEPLSTIVVSKLHADFFYLARLIGIEIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSEILYWANTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
'Caldanaerobacter subterraneus tengcongensis_NP_624062.1'   --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSVELFFHIFKNPLIYYITLAVLIAGLIFALLKEKLKIGVEKVADKISLRLFAFIIIVILGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAALTPVGEPLATIVVSKLHADFFYLARLIGIEIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIREVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSEILYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
'Caldanaerobacter subterraneus yonseiensis_ERM91218.1'      --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFRAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPVIDLYIVKMKSEILYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
'Caldicellulosiruptor bescii YP_002573898.1'                --------------------------------------------MIAGLIILLLVILFIPFLVKAVEHNLEYFLFVMGIIGVIISKQMNLKLFEHILQNKLLYYITFAVLIAGMLFFFFRNKINRLIDVLTNKISIQIFTFIIIVILGLSSSFITAIIASLLLTEIMHHTPLERNTKLKVIVLACFAIGFGAALTPVGEPLATITISKLKADFFYLARAIGFEIIITILLMAFLAALIVKKANKV-DKDEYIENTEGIKDVFLRAFKVFVFVFALELLGTAFKPLIDLYIIKLDAKILYWVNMISAIVDNATLAAAEVSKEMTNEQVRAIILGMIISGGMLIPGNIPNIISAGKFKIKSKEWAKIGVPMGLILMVIYFIMVFIVKV
'Caldicellulosiruptor hydrothermalis YP_003991814.1'        --------------------------------------------MITGLIVLLLIILFLPFFVKAVEHNLEYFLFIMGIIGVIISKQMSLDLIEHIFKNRLLYYITFAVLIAGMLFFFFRDKINRMIELLTHKISIQLFIFIVIIMLGLSSSFITAIIASLLLTEIMHHMPLDRNTKLKVIVLACFAIGFGAALTPVGEPLATITISKLKADFFYLARAIGLEIIITILLMACLAALVVKKANKI-DKDEFIENTEGIKDVFLRAFKVFIFVFALELLGTAFKPLIDLYIIKLDAKILYWVNMISAIVDNATLAAAEISKDMTNEQVRAIILGMIVSGGMLIPGNIPNIISAGKFKIKSKEWAKIGVPIGLILMAVYFVLVFVLKV
'Caldicellulosiruptor kronotskyensis YP_004023322.1'        --------------------------------------------MIAGLIILLLVILFIPFLVKAVEHNLEYFLFVMGIIGVIISKQMNLKLFEHILQNKLLYYITFAVLIAGMLFFFFRNKINRLIEVLTNKISIQIFTFIIIVILGLSSSFITAIIASLLLTEIMHHTPLDRNTKLKVIVLACFAIGFGAALTPVGEPLATITISKLKADFFYLARAIGFEIIITILLMAFLAALIVKKANKV-DKDEYIENTEDIKDVFLRAFKVFVFVFALELLGTAFKPLIDLYIIKLDAKILYWVNMISAIVDNATLAAAEVSKEMTNEQVRAIILGMIISGGMLIPGNIPNIISAGKFKIKSKEWAKIGVPMGLILMVIYFIMVFIVKV
Thermoanaerobacter_ethanolicus_EGD52029.1                   --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
Thermoanaerobacter_siderophilus_EIW00263.1                  MSMPLSYEYYTTKTLCNTPGAPQKLMFVFIYSFVSKYILQGGIYMVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
Thermoanaerobacter_siderophilus_EIW00539.1                  --------------------------------------------MVIALFVILVLILLLPFMVKQVEHNLEYFLFTMGIISVIVSKQFSIELFLHIFKNPLIYYITLAVLIAGLVFTLFKEKLKIGMEKITDKISLRLFAFIIIVFLGLMSSIITAIIASLVLVEIVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLNADFFYLARLIGIDVIIAVVILGLIGAFFAKRESGTTNFMKDIDANENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPAMTQEQVRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGGILLLVYYVVLFVI--
Thermoanaerobacter_thermohydrosulfuricus_EMT39667.1         --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKVNLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
'Thermoanaerobacter wiegelii YP_004818845.1'                --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSVELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVA--VSLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGVDIIIAILVLGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPVIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARIAVPLGAILLIVYYIVLFVI--
'Thermoanaerobacter wiegelii YP_004818850.1'                --------------------------------------------MVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVAEKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENTKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
'Thermoanaerobacter wiegelii YP_004820398.1'                MSMPLSYEYYTTKTLCNTPGAPQKLMFVFIYSFVSKYILQGGIYMVTALVVILVLILLLPFVVKQVEHNLEYFLFTMGIISVIVSKQFSAELFFHIFKNPLIYYITLAVLIAGLIFTLLKEKLKIGVEKVADKISLRLFAFIIIVVLGLMSSIITAIIASLVLVEVVNYLPLTRKNKINLIVIACFSIGLGAVLTPVGEPLATIVVSKLHADFFYLARLIGIDIIIAILALGLIGTFFAKRESGIGEPTEDVEADENIKEVFIRAFKVFVFIFALELLGTGFKPIIDLYIVKMKSELLYWVNTISAIVDNATLAAAEISPSMTPEQIRAILMGMLISGGMLIPGNIPNIISAGKLKIKSTEWARTAVPLGAILLIVYYIVLFVI--
;
END;

[ The following blocks are output data for analysis step 16723 ]
BEGIN TREES;
      TITLE 11565_phylogeny;
      LINK TAXA = TaxaForAnalysisStep16723;
      TREE 11565_ML = [&R] (((((((Thermoanaerobacter_thermohydrosulfuricus_EMT39667.1:0.002957,(Thermoanaerobacter_ethanolicus_EGD52029.1:1.0E-6,'Thermoanaerobacter wiegelii YP_004818850.1':0.00296)0.0000:1.0E-6)0.0000:1.0E-6,Thermoanaerobacter_siderophilus_EIW00263.1:1.0E-6)0.0000:1.0E-6,'Thermoanaerobacter wiegelii YP_004820398.1':1.0E-6)0.7430:0.003025,(('Caldanaerobacter subterraneus tengcongensis_NP_624062.1':0.008904,'Caldanaerobacter subterraneus pacificus_EEB75482.1':0.005918)0.9270:0.008958,'Caldanaerobacter subterraneus yonseiensis_ERM91218.1':0.005866)0.7650:0.002983)0.4110:0.00603,'Thermoanaerobacter wiegelii YP_004818845.1':0.008867)0.8640:0.039017,Thermoanaerobacter_siderophilus_EIW00539.1:0.069473)1.0000:0.2591685,('Caldicellulosiruptor hydrothermalis YP_003991814.1':0.046194,('Caldicellulosiruptor bescii YP_002573898.1':0.005827,'Caldicellulosiruptor kronotskyensis YP_004023322.1':0.002963)0.9490:0.072968)1.0000:0.2498465)root;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr89886]


END;