#NEXUS
[written Tue May 26 10:22:50 SGT 2015 by Mesquite  version 3.03 (build 702) at Mesemite.local/192.168.1.2 (William Piel)]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=38;
	TAXLABELS
		Arthrobacter_sp._A0JUZ7 Mycobacterium_smegmatis_A0QX85 Thermosinus_carboxydivorans_A1HMG5 Arthrobacter_aurescens_A1R562 Nocardioides_sp._A1SL57 Janibacter_sp._HTCC2649_A3TLY4 marine_actinobacterium_PHSC20C1_A4AHK5 Geobacillus_thermodenitrificans_A4ISR3 Desulfotomaculum_reducens_A4J708 Salinispora_tropica_A4X9Q0 Clavibacter_michiganensis_subsp._Michiganensis_A5CSK6 Pelotomaculum_thermopropionicum_A5CZ74 Dehalococcoides_mccartyi_A5FQ03 'Bacillus sp. SG-1 A6CND9' Kineococcus_radiotolerans_A6WCU8 Bifidobacterium_adolescentis_A7A8P7 Dehalococcoides_sp_A8CRG7 Renibacterium_salmoninarum_A9WQA3 Heliobacterium_modesticaldum_B0TDM8 Desulforudis_audaxviator_B1I557 Mycobacterium_abscessus_B1MBX5 Clostridium_butyricum_B1QTN6 Geobacillus_sp._B1SQW0 Rhodococcus_erythropolis_B1VDA6 Streptomyces_griseus_subsp._Griseus_B1W0M4 Bifidobacterium_sp._B2EB57 Kocuria_rhizophila_B2GKF8 Acidimicrobium_ferrooxidans_C7LZ82 Marine_metagenome_CAM1 Actinomyces_viscosus_C505_F2UUE1 Actinomyces_naeslundii_J2ZMD0 Rhodococcus_jostii_Q0SHY5 Moorella_thermoacetica_Q2RGW1 Dehalococcoides_mccartyi_Q3Z6V7 Thermobifida_fusca_Q47QS4 Leifsonia_xyli_subsp._Xyli_Q6AE15 Bifidobacterium_longum_Q8G4S5 Bacillus_halodurans_Q9K6Z5 
	;

END;


BEGIN CHARACTERS;
	TITLE  'Phylogenetic analysis of HisA / PriA evolutionary intermediates';
	DIMENSIONS  NCHAR=250;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	Arthrobacter_sp._A0JUZ7                                -LELLPAVDVVNGQAVRLVQGEAGSETSYGTPLEAALNWQEQGAEWVHLVDLDAAFGRGSNAELLREVVGRLDIKVELSGGLRDDESLEKALDLGVARVNLGTAALENPEWTARAIDRFGDKIAVGLDVRGTTLAGRGWTKEGGDLWDVLARLEEAGCARYVVTDVTKDGTLQGPNVELLRKMVERTGKPVVASGGISSLEDLKVLRSLVPLGVEGAIVGKALYAGAFTLPEALDVAG------------
	Mycobacterium_smegmatis_A0QX85                         -LILLPAVDVVNGQAVRLVQGKAGSETDYGSAIEAAEAWQRDGAEWIHLVDLDAAFGRGSNRELLAEVVGKLDVAVELSGGIRDDESLRAALDTGCARVNIGTAALENPQWCARAIAEHGDRVAVGLDAGGFRLRGRGWETDGGDLWEVLDRLDSEGCSRYVVTDVSKDGTLTGPNLDLLAAVAGRTDAPVIASGGVSSLDDLRAIATLTGVGVEGAIVGKALYAGRFTLPQALSAVS------------
	Thermosinus_carboxydivorans_A1HMG5                     -MIVFPAIDIRGGKCVRLTEGRFDAETVFSNPVEVAKRWRREGAEYLHVVDLDGAVGRPVNLELVIAIAKKVDIPVQLGGGIRTMDTIDTVLAAGISRIILGSVAVRQPALVKEACARYGDRIVVGIDARDGVVAVEGWGVSGQGAEELARQMAAVGVARIIYTDISRDGTLTGINVEATCALACAAGVPVIASGGLRGLDDIRALWQARTAGIEGVIAGKALYTGALSLRSAIRVAK------------
	Arthrobacter_aurescens_A1R562                          -LELLPAVDIVDGQAVRLLQGEAGSETSYGTPLEAALNWQNDGAEWVHMVDLDAAFGRGNNAALISDVVSQLNVKVELSGGLRDDESLERALELGVARVNLGTAALENPEWTRKAIDRFGDKIAVGLDVRGTTLAGRGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLQGPNVELLRQMVEKTGKPVVASGGISSLEDLRVLRELVPLGVEGAIVGKALYAGAFTLPEALDVAG------------
	Nocardioides_sp._A1SL57                                -LELLPAVDITEGRAVQLAQGVAGSERTYGDPVAAAMRWQEAGAEWIHLVDLDAAFGRGSNRELQAEIVGALDVQVEMSGGIRDDESLAAALATGCRRVNIGTAALEQPEWCRRVIAEHGDRVAIGLDVRGRTLAARGWTKDGGDLYETLARLDAEGCARYVVTDVNKDGMLQGPNLQLLRDVCAATSAPVVASGGVTTLADIEALMELVPVGVEGAIAGTALYEGRFTLEDALALTR------------
	Janibacter_sp._HTCC2649_A3TLY4                         -LQLLPAVDVAGGRAVQLVQGVAGSGGEFGEPVEAALRWQEQGAEWLHLVDLDAAFGRGDNAELLAQIVGQLDIDVEMSGGIRDAETLERALATGCRRVNLGTAALENPEWTASAIAEHGDRIAVGLDVRGTTLAARGWTQEGGDLWETLERLDAEGCARYVVTDVNKDGMLKGPNLDLLRDVCTRTDRPIIASGGVSTLADIEALRTMVGEGVEGAITGSALYRGAFTLPDALDVAG------------
	marine_actinobacterium_PHSC20C1_A4AHK5                 -LTLLPAVDVADGKAVRLTQGEAGTEKSYGDPCAAAHDWVDQGAEWIHLVDLDAAFGRGNNQAMIKKVIKSTRVNIELSGGIRDDESLEAALATGAKRINLGTAALENPEWAAHVIAEYGEAIAVGLDVRGTTLAARGWTQEGGDLWTVLERLEAAGCCRYVVTDVTKDGTLQGPNVELLRQVMERTHRPVIASGGVSSLDDLIELRELVPQGLEGAIVGKALYAKAFTLAEALDVSS------------
	Geobacillus_thermodenitrificans_A4ISR3                 -FTIYPAIDMRGGKCVRLLQGDYNKETVYGSPVAMAEQFAAQGAEWIHMVDLDGAKGRRVNDRFVIEAANRLSVNVQVGGGIRTEEDVAYYLERGVARVILGSAAISNPTFVKKMLQTYGRRIVIGIDARDGFVATEGWLETSNKAEELGQMLAEAGAETFIFTDIATDGTLSGPNITAAVRLAEATGKEVIASGGVRSLDDLRALREYAEQGIGGAIVGKALYTNQFTLAEALKAVN------------
	Desulfotomaculum_reducens_A4J708                       -MILFPAIDLKEGQCVRLVEGRMDSATVYSDPGSMARLWQDQGAQYIHVVDLDGAFGQPRNRQSIAQIVQGVQVPVQVGGGIRDLETIEDLLSLGVDRVILGSAAILKPELVAEACRKYGQRILLGIDAKDGQVAIQGWGETVKTALDLALEMKQLGIERAVFTDIRRDGKLSGPNLAATGELARNSGLRVIASGGVASLEDIRQLKKLEQDGVEGAILGKALYTNAVKLPEALVIAR------------
	Salinispora_tropica_A4X9Q0                             -LTLLPAVDVADGQAVRLVQGAAGSETVYGDPFDAALAWQRDGAEWIHLVDLDAAFGRGSNAELLADVVRRLDVRVELSGGIRDDASLQAALATGAARVNIGTAALEDPQWCDRVCGEYGDRVAIGLDVRGQTLSARGWTRDGGDLWEVLARLDRAGASRYVVTDITKDGTMRGPNLGLLREVCARTNAPVIASGGISTLADLRALAALEPVGVEGVIAGKALYAGAFTVAEALRTLA------------
	Clavibacter_michiganensis_subsp._Michiganensis_A5CSK6  -LTLLPAVDVAGGQAVRLTQGAAGTETGYGDPVDAARDWAEQGAEWLHLVDLDAAFGRGDNLSVISRVIRAIGVQIELSGGIRDDRSLDVALESGATRINLGTAALENPEWAASVIAQHGEAVAVGLDVRGRTLSARGWTQDGGDIWEVLERLEDAGCARYVVTDVTKDGTLQGPNLQLLRDVLERTERPVVASGGVSSLDDIQALRELVPLGLEGAIVGKALYAGAFTLGEALDVAG------------
	Pelotomaculum_thermopropionicum_A5CZ74                 -MLIIPAIDLREGNCVRLVEGRLDRETVYSDPVAVAGMWQSQGARMLHVVDLDGAFGAPKNLDVIGEILSAVSIPVQVGGGIRSMEAVERLLELGAARVILGTAAILKPQLVAEACARYGEAVLVGIDGRNGRVAIEGWGVTVDGTVELALEMKRLGIKRAVFTDIRRDGTLRGPNLEAIREFAAATGLKVIASGGVSNAEDLRALKKLEPLGVEAVIMGKALYAGTVKMSEALAIAS------------
	Dehalococcoides_mccartyi_A5FQ03                        -IEIIPAIDILGGRCVRLFQGDYAQETVYSDPVGTAMRWQSLGAPRLHVVDLDGAAGQSVNFELIKEIANSALIPVEVGGGIRSMETVKKLLVAGVDRVILGTAAVENPELVKEICARYADSVAVSIDARNGKVATRGWVTNTEDALELARSMKKLGIRRFIYTDISRDGTLSEPNFAAIRDLISAINVPVIASGGVSSLSHLRLLKDI---GAEGAIVGKAIYTGDLNLKRAFEDLS------------
	'Bacillus sp. SG-1 A6CND9'                             -FTIYPAIDMRGGKCVRLLQGDYSKETVYGSPFDMAKRFVDEGAQWIHMVDLDGAKGSRVNDKFVIAVANELGAKVQIGGGIRSEEDIEYYLNNGVQRVIIGSLAVSQTELVKSWLAKYGDRIAIGLDAKDGFVATHGWIETSQKAVDLGVELAQAGAETFIFTDIATDGMLSGPNVEAVAELAKATGKEVIASGGVSSMDDLRLLKEYEGKGVAGAIVGKAIYTGKVSVEDAVKEVS------------
	Kineococcus_radiotolerans_A6WCU8                       -LELLPAVDVADGQAVRLVQGEAGSETFYGAPLDAALAWQEAGAEWVHLVDLDAAFGRGSNRELLAEVVGRLDVAVELSGGIRDDASLEAALATGCRRVNLGTAALEDPDWTRSAIARHGDRIAVGLDVRGTTLAARGWTREGGDLWEVLARLDADGCARYVLTDVTKDGTLRGPNTDLLREVCARTQAPVVASGGVSSLEDLRVLRGLVDLGVEGAIVGKALYAGNFTLPQALDVAG------------
	Bifidobacterium_adolescentis_A7A8P7                    -LTLLPAVDVRDGKAVRLRQGESGSETDYGSPLEAARTWVESGAEWIHLVDLDAAFGTGNNRDQLRAIVKELKVNIEMSGGVRDDASLDAALEAGAARVNIGTAALENPDWTASVIKKYGDRVAVGLDVRGHTLAARGWVKEGGDLFETMKFLDSVGCSRYVVTDVARDGMMSGPNIELLREVASRTDAKVTASGGISKLDDLRNIKELAELGVDAAILGKSLYARAFTLEEALEVAR------------
	Dehalococcoides_sp_A8CRG7                              -IEIIPAIDILGGRCVRLLQGDYAQETVYSDPVGTAMRWQSLGAPRLHVVDLDGAAGESVNFELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTAAVENPELVREICARYADSVAVSIDARNGKVATRGWVNSTEDALELARSMKKLGVKRFIYTDISRDGTLSEPNFAAIRDLISAINMPVIASGGVSNLSHLRLLKDI---GAEGAIVGKAIYTGDLNLKRAFEELS------------
	Renibacterium_salmoninarum_A9WQA3                      -LELLPAVDVADGQAVRLVQGEAGSETSYGAPIDAALAWQQDGAEWVHLVDLDAAFDRGSNLALLRDVVAQLNVKVELSGGIRDDASLEGALKLGAERVNLGTAALEDPVWTARAIERFGDKIAVGLDVRGTTLAARGWTKDGGDLWEVLARLEDAGCARYVVTDVTKDGTLRGPNIELLQQMLERTDRPVVASGGVSSLDDLVQLRALVPHGLEGAIVGKALYAGAFTLPEALDVAG------------
	Heliobacterium_modesticaldum_B0TDM8                    -MLIFPAIDLKGGRCVRLYQGRMEDAIVYNDPVSQALAWQAKGAQMIHLVDLDGAFGEPKNLPVIQAILEAVTVAVQLGGGIRDLNIIDRYLRMGVSRVIIGTAAIKNPELLSVACKEYGQRIVLGLDARDGKVATDGWAGTSQTALELALEMKGRGLRRVVYTDISKDGTLAGPNLAATAELARATGLKVIASGGFATIDDVKAAAALEGDGIEGAILGKSIYTGAIDVAEAIRVAR------------
	Desulforudis_audaxviator_B1I557                        -MLIIPAVDLRGGRCVRLFQGRADQETVYSDPVAVARTWEEQGARRLHVVDLDGAFGKPQNSGVVLDIVKSVNIPVQVGGGIRNPENVKCYLEHGVDRVILGTAALTNPEFLDAVVAAYGERIVVGVDCRDGRVCVQGWEQTAADVLPFLEELVRRGVRRVVFTDVKRDGTLEGPNLEEIARVAAHTELKVIASGGVSRLEDLRALKKLEHLGVDSVIIGKALYAGTITLAEALALER------------
	Mycobacterium_abscessus_B1MBX5                         -LVLLPAVDVADGQAVRLVQGKAGSETTYGSPRDAALAWQNDGAEWVHLVDLDAAFGRGSNRELLAQVVGELDVKVELSGGIRDDEALTAALATGCARVNLGTAALEDPEWCASAIARHGERVAVGLDVGAHRLRGRGWVSDGGDLWEVLERLRAQGCSRYVVTDVTKDGTLTGPNLELLAQVAGVANAPVIASGGVSSLDDLRAIAELTGAGVEGAIVGKALYAGRFTLPDAIAAVS------------
	Clostridium_butyricum_B1QTN6                           -MIILPAIDIIDGKPVRLYQGDYDKKEIVADIFETAKSFEKMGAEYIHLVDLDGAKGSNDNHELVIKIANMLDIPVELGGGIRSFETIKYLLENGVSRVILGTIAMEDENLLKRAISEYGEKIAVGIDCKDGKVYGRGWLEGSNDYIEFAQKMESLGVKNIIVTDISKDGTLQGPNLDMLKKIKETVNIDITASGGIRDIENIKDLNEI---GLYGAITGKAIYAETLSLEEAIKAVR------------
	Geobacillus_sp._B1SQW0                                 -FTIYPAIDMRGGKCVRLLQGDYHKETVYGSPVEMAAFFAEQGAEWIHMVDLDGAKGKRINDQFVVEVAKQLPVKVQIGGGIRTEDDIVYYLENGVARVILGSAAIADPPFVKEMLKKYGERIAIGIDAKNGFVATEGWLNTSNKATDLGKELAEAGAQTFIFTDIATDGMLSGPNIQAVVEMARATEKHVIASGGVSSLEDLVSLQTYADAGVVGAIVGKALYTKKFTVAEALKVVQ------------
	Rhodococcus_erythropolis_B1VDA6                        -LVLLPAVDVVNGEAVRLVQGEAGSETGYGSPRDAALAWQNDGAEWVHLVDLDAAFGRGSNSELLAGVIGDLTVKVELSGGIRDDASLEAALATGCARVNLGTAAIEDPEWCARALAKYGDKIAVGLDVGQYRTRGRGWVTDGGDLWETLARLDRDGCTRYVVTDVSKDGTLTGPNLELPSQVCAVTDAHVVASGGVSTIEDLLAISSLVDQGVEGAIVGKALYAGRFTLPEALAAVS------------
	Streptomyces_griseus_subsp._Griseus_B1W0M4             -LELLPAVDVRDGQAVRLVHGESGSETSYGSPLEAALAWQSAGAEWLHLVDLDAAFGTGDNRALIAEVAGAMDIKVELSGGIRDDASLAAALATGCRRVNLGTAALETPEWVAKVIAEHGDKIAVGLDVRGTTLRGRGWTRDGGDLYETLARLDSEGCARYVVTDIAKDGTLEGPNLGLLRDVCAATDRPVVASGGVSSLDDLRAISLLVPEGVEGAIVGKALYAKAFTLEEALKAVA------------
	Bifidobacterium_sp._B2EB57                             -LTLLPAVDVRDGKAVRLRQGESGSETDYGSPLDAARTWVDAGAQWIHLVDLDAAFGTGDNRAQLREIVRQLKVNIEMSGGVRDDASLDAALDAGAARVNIGTAALENPEWTARVIDKYGDKVAVGLDVRGHTLAARGWVKEGGGLFETMRFLDDAGCSRYVVTDVTRDGMMSGPNIDLLREVAERTDARVTASGGISKLDDLRAIKELLPLGVDSAILGKSLYAGAFTLEEALAVAN------------
	Kocuria_rhizophila_B2GKF8                              -LELLPAVDVQGGQAVRLVQGEAGSETGYGDPLEAARAWQDAGAEWLHLVDLDAAFGRGDNIEVLRHVAENLDLKIEMSGGIRDDESLERVLSLRPARINLGTAALENPQWTHRVIAEHGDLIAVGLDVRGTTLAARGWTEEGGDLWEVLERLEADGCARYVVTDVTKDGTLRGPNTELLAEVARRTDKPVVASGGISSLEDIAALRELVPSGVEGAIVGKALYAGRFTLAQALDVAG------------
	Acidimicrobium_ferrooxidans_C7LZ82                     -MELVVAVDLLDGEAVRLRQGRFDAPRRFGDPRRYVEGALDAGARWFHVVDLDRARGDRRNADMVGDLVREAGGSVEVGGGVRTARDIAELLETGASRVVLGTALVEE------TLDELPEHLVAALDYGALEVVVSAWERSGGRLLEASARLFARGVRTQLLTDVGRDGMASGPDLGTYQGLCEVVPVEVIASGGVASADDLAKLAAIRGAAVWGAVVGTALLDGSLGFDEALSACR------------
	Marine_metagenome_CAM1                                 -FALLPAVDVAEGRAVRLVQGAAGTETDYGDPVAAARSWVEQGAPWIHLVDLDAAFGRGDNRAVVHRVVQAVDVHVEVAGGIRDDASLDAALASGASRAVIGTAAMENPDWVRSAIDRYGDRLAVSLDVRGHTLAARGWTTEGGDLFETIGRLDADGCARYIVTDVEKDGMMHGPNLHLLKKVCDHTTLPP-----------------------------------------------------------
	Actinomyces_viscosus_C505_F2UUE1                       MLTLLPAVDVADGKAVRLLQGEVGSETDYGSPVDAARDWVRAGAEWIHLVDLDAAFGRGSNHELLARIVGEVGIKVELSGGIRDDASLARALAAGAARVNLGTAALEDPEWTERVIAEHGEKIAVGLDVRGSTLAARGWTKEGGDLWETLERLNAAGCARYVVTDVTRDGTLSGPNTELLTEVCQRSPAPVVASGGIAHLDDLVALRRLVPLGLEGAIVGKALYNGNFTLQEALAVAG------------
	Actinomyces_naeslundii_J2ZMD0                          MLTLLPAVDVADGKAVRLLQGEVGSETDYGSPVDAARDWVRAGAEWIHLVDLDAAFGRGSNSELLSRIVGEVGIKVELSGGIRDDASLARALAAGAARVNLGTAALEDPEWTERVIAEHGDKIAVGLDVRGTTLAARGWTKEGGDLWETLERLNAAGCARYVVTDVTRDGTLSGPNTTLLTEVCQRSPAPVVASGGIAHLDDLVALRRLTPLGLEGAIVGKALYNGNFTLQEALAVAG------------
	Rhodococcus_jostii_Q0SHY5                              -LVLLPAVDVVNGEAVRLVQGEAGSETGYGSPRDAALAWQNDGAEWVHIVDLDAAFGRGSNRELLADVVGELDVQVELSGGIRDDASLEAALATGCGRVNLGTAAIENPEWCARAIAKYGEKIAVGLDVGEYQLRGRGWVTEGGNLWETLARLDKDGCSRYVVTDVSKDGTLTGPNLELLAQVCAATDAPVVASGGVSTIDDLRAIAGLVDQGVEGSIVGKALYAGRFTLPEALAAVS------------
	Moorella_thermoacetica_Q2RGW1                          -MLVMPAIDLREGRCVRLYQGRIEAETVYSDPVAVARGWVERGARWLHVVDLDGAFGRPRNLEVIAAIIRAAGVPVQVGGGIRSLESLAGVLAAGASRVVLGTVAITNPEVVATAVERYGERVVVGIDSLDGQVAIEGWEATVAGAVEFARQMASLGVTRAVFTDIGRDGTLQGPNIAATREMARSGGLKIIASGGIASLDDLRKLKELAAEGVEGAILGRSLYNGNFTLEEALAVAA------------
	Dehalococcoides_mccartyi_Q3Z6V7                        -MEIIPAIDILGGRCVRLLQGDYAQETVYSDPVGTAMRWQSLGAPRLHVVDLDGAAGESVNFELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARYADSVAVSIDARNGKVATRGWVNSTEDALELARSMKKLGVKRFIYTDISRDGTLSEPNFAAIRDLISAINMPVIASGGVSSLSHLRLLKDI---GAEGAIVGKAIYTGDLNLKRAFEELS------------
	Thermobifida_fusca_Q47QS4                              -LELLPAVDVAGGQAVQLVQGKDGTGGRYGDPLNAALTWQNAGAEWIHLVDLDAAFGRGHNRELLASIVGKLDIKVELSGGIRDDESLNAALATGCHRVNIGTAALENPDWCAKVIAEHGDRVAIGLDVRGTTLAARGWTRDGGDLYETLERLEAAGCARYIVTDVNKDGTLKGPNLDLLRDVCSRTDKPVVASGGISSLDDLRALAALVPEGVEGAIMGTALYEGAFTLEEALATVR------------
	Leifsonia_xyli_subsp._Xyli_Q6AE15                      -LVLLPAVDVADGKAVRLTQGAAGSETSYGDPVDAAAEWADAGAEWIHLVDLDAAFGRGDNRGLLKRVIRQTGVKIELSGGIRDDDSLEHALEIGATRVNLGTAALENPEWASHVIGQYGEAIAVGLDVRGTTLAARGWTREGGDLWQVLERLEEAGCARYVVTDVTKDGALKGPNLDLLRQVVERTERPVVASGGIASLDDIAALRELVSLGVEGAIVGKALYSGAFTLPEALDVAG------------
	Bifidobacterium_longum_Q8G4S5                          -LTLLPAVDVRDGKAVRLRQGESGSETDYGSPFEAARTWVEAGAEWIHLVDLDAAFGTGNNRDQLREIVHELRVNIELSGGVRDDASLDAALEAGAARVNIGTAALENPDWTASVIKKYGDRVAVGLDVRGHTLAARGWTREGGDLFETMKFLDSVGCSRYVVTDVAKDGMMSGPNIQLLSEVAERTDAKVTASGGISKLDDLRAIKELAEIGVDSAILGKSLYARAFTLQEALEVAK------------
	Bacillus_halodurans_Q9K6Z5                             -FIIYPAIDMRDGKCVRLVQGDYNQETVYGSPFTMAKSFAEQGAEWIHMVDLDGAKKERMNHEHVVKVATELDVNVQVGGGIRTAEDIAYYLDRGISRVILGSVAVNNPAFTKEMLQKYGEKIAIGLDARDGYVATEGWLETSSKAETLGQELARHGAEVFIFTDISRDGMLSGPNTEAIVQLAKATGKQVIASGGVSSLQDLDALRNEKQNGIAGAIVGKALYTNQFTLEDALKEES------------

;


END;

BEGIN TREES;
	Title 'Phylogenetic analysis of HisA / PriA evolutionary intermediates';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 Arthrobacter_sp._A0JUZ7,
[1] 		2 Mycobacterium_smegmatis_A0QX85,
[2] 		3 Thermosinus_carboxydivorans_A1HMG5,
[3] 		4 Arthrobacter_aurescens_A1R562,
[4] 		5 Nocardioides_sp._A1SL57,
[5] 		6 Janibacter_sp._HTCC2649_A3TLY4,
[6] 		7 marine_actinobacterium_PHSC20C1_A4AHK5,
[7] 		8 Geobacillus_thermodenitrificans_A4ISR3,
[8] 		9 Desulfotomaculum_reducens_A4J708,
[9] 		10 Salinispora_tropica_A4X9Q0,
[10] 		11 Clavibacter_michiganensis_subsp._Michiganensis_A5CSK6,
[11] 		12 Pelotomaculum_thermopropionicum_A5CZ74,
[12] 		13 Dehalococcoides_mccartyi_A5FQ03,
[13] 		14 'Bacillus sp. SG-1 A6CND9',
[14] 		15 Kineococcus_radiotolerans_A6WCU8,
[15] 		16 Bifidobacterium_adolescentis_A7A8P7,
[16] 		17 Dehalococcoides_sp_A8CRG7,
[17] 		18 Renibacterium_salmoninarum_A9WQA3,
[18] 		19 Heliobacterium_modesticaldum_B0TDM8,
[19] 		20 Desulforudis_audaxviator_B1I557,
[20] 		21 Mycobacterium_abscessus_B1MBX5,
[21] 		22 Clostridium_butyricum_B1QTN6,
[22] 		23 Geobacillus_sp._B1SQW0,
[23] 		24 Rhodococcus_erythropolis_B1VDA6,
[24] 		25 Streptomyces_griseus_subsp._Griseus_B1W0M4,
[25] 		26 Bifidobacterium_sp._B2EB57,
[26] 		27 Kocuria_rhizophila_B2GKF8,
[27] 		28 Acidimicrobium_ferrooxidans_C7LZ82,
[28] 		29 Marine_metagenome_CAM1,
[29] 		30 Actinomyces_viscosus_C505_F2UUE1,
[30] 		31 Actinomyces_naeslundii_J2ZMD0,
[31] 		32 Rhodococcus_jostii_Q0SHY5,
[32] 		33 Moorella_thermoacetica_Q2RGW1,
[33] 		34 Dehalococcoides_mccartyi_Q3Z6V7,
[34] 		35 Thermobifida_fusca_Q47QS4,
[35] 		36 Leifsonia_xyli_subsp._Xyli_Q6AE15,
[36] 		37 Bifidobacterium_longum_Q8G4S5,
[37] 		38 Bacillus_halodurans_Q9K6Z5;
	TREE con_50_majrule = (20:0.2896643000000001,((33:0.29570260000000004,((12:0.20979100000000006,(9:0.1909537,19:0.4082272):0.13305849999999997):0.07371872000000002,(3:0.3964993,(22:0.6132995,(34:0.0041222659999999856,(13:0.047034279999999984,17:0.0066068369999999765):0.009837147000000046):0.3526827,(38:0.18781479999999995,(8:0.1155583,(23:0.16543469999999993,14:0.225553):0.04483647000000002):0.06257646000000006):0.35068979999999994):0.09197047000000003):0.16806180000000004):0.048839580000000105):0.1620919999999999,(28:1.154607,(29:0.26065270000000007,((26:0.04054126000000002,(37:0.04442308000000006,16:0.027745850000000072):0.06510175000000007):0.15478999999999998,((31:0.015953490000000015,30:0.013013280000000016):0.16187150000000006,(((18:0.10318889999999992,(4:0.060341179999999994,1:0.05059944000000005):0.06596125999999991):0.06112845000000011,(27:0.1752623000000001,(36:0.08163195999999995,(7:0.14362439999999999,11:0.12623549999999994):0.05734405999999992):0.10494330000000007):0.04201739999999998):0.03871374999999999,(15:0.10372569999999992,((10:0.21764650000000008,(35:0.11294540000000008,(6:0.18638390000000005,5:0.14271980000000006):0.07475137999999992):0.06924526999999991):0.02457318999999991,(25:0.1540534,((24:0.0770024199999999,32:0.042796499999999904):0.06878987000000003,(2:0.1212245999999999,21:0.09355073999999997):0.052188789999999985):0.10400359999999997):0.03784589999999999):0.043522629999999896):0.04234298999999997):0.05422040000000006):0.07261932999999998):0.10809630000000003):0.3987019999999999):0.28171040000000014):0.14483215);

END;


BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED  (CHARACTERS = 'Phylogenetic analysis of HisA / PriA evolutionary intermediates')  =  unord:  1 -  250;

END;

BEGIN CODONS;
	CODESET * UNTITLED  (CHARACTERS = 'Phylogenetic analysis of HisA / PriA evolutionary intermediates')  =  universal:  1 -  250;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED  (CHARACTERS = 'Phylogenetic analysis of HisA / PriA evolutionary intermediates')  =  'Mk1 (est.)':  1 -  250;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1432606970814;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 4680680381862729937;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 2478222894556822634;
			mqVersion 303;
			checksumv 0 3 4096429931 null  getNumChars 250 numChars 250 getNumTaxa 38 numTaxa 38   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 7.288665660552E13 sumSquares 7.288665660552E13 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 143;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 1122 663;
			setLocation 8 23;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #4680680381862729937  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 1279.1432606965325.5012772864166433415;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 979 591;
					setLocation 8 23;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setActive;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.SquareLineTree.SquareLineTree;
					tell It;
						setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							branchLengthsToggle off;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter on;
							toggleEven on;
							setFixedTaxonDistance 0;
						endTell;
						setEdgeWidth 4;
						showEdgeLines on;
						orientUp;
					endTell;
					setBackground White;
					setBranchColor Black;
					showNodeNumbers off;
					showBranchColors on;
					labelBranchLengths off;
					centerBrLenLabels on;
					showBrLensUnspecified on;
					showBrLenLabelsOnTerminals on;
					setBrLenLabelColor 0 0 255;
					setNumBrLenDecimals 6;
					desuppress;
					getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
					tell It;
						setColor Black;
						toggleColorPartition off;
						toggleColorAssigned on;
						toggleShadePartition off;
						toggleShowFootnotes on;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 1;
					setDrawingSizeMode 0;
					toggleLegendFloat on;
					scale 0;
					toggleTextOnTree off;
					showWindow;
				endTell;
				desuppressEPCResponse;
				getEmployee #mesquite.trees.ColorBranches.ColorBranches;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
				tell It;
					setAlwaysOn off;
				endTell;
				getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
				tell It;
					colorByPartition off;
				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles;
				tell It;
					setOn on;
					setDigits 4;
					writeAsPercentage off;
					toggleCentred off;
					toggleHorizontal on;
					toggleWhiteEdges on;
					setFontSize 10;
					setOffset 0  0;
				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings;
				tell It;
					setOn on;
					toggleCentred on;
					toggleHorizontal on;
					setFontSize 10;
					setOffset 0  0;
				endTell;
				getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #2478222894556822634 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 979 591;
					setLocation 8 23;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					colorCells  #mesquite.charMatrices.ColorByState.ColorByState;
				tell It;
					setStateLimit 9;
					toggleUniformMaximum on;
				endTell;
					colorRowNames  #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
					colorColumnNames  #mesquite.charMatrices.CharGroupColor.CharGroupColor;
					colorText  #mesquite.charMatrices.NoColor.NoColor;
					setBackground White;
					toggleShowNames on;
					toggleShowTaxonNames on;
					toggleTight off;
					toggleThinRows off;
					toggleShowChanges off;
					toggleSeparateLines off;
					toggleShowStates on;
					toggleAutoWCharNames off;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					toggleBirdsEye off;
					toggleShowPaleGrid off;
					toggleShowPaleCellColors off;
					toggleShowPaleExcluded off;
					togglePaleInapplicable on;
					toggleShowBoldCellText off;
					toggleAllowAutosize off;
					toggleColorsPanel off;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
				endTell;
				getWindow;
				tell It;
					forceAutosize;
				endTell;
				hideWindow;
				getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
				tell It;
					togglePanel off;
				endTell;
				getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
				tell It;
					autotabOff;
				endTell;
				getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
				tell It;
					gapCosts 8 3 2 2;
					subCosts  5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5;
				endTell;
				getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		endTell;
end;