NEXUS
[File created by TreeBASE:  7/26/07  21:06:00]
[Matrix accession#: M1993]

BEGIN TAXA;
	TITLE M1993;
	DIMENSIONS  NTAX=28;
	TAXLABELS
		Hydrogenobacter_thermophilus	Helicobacter_pylori	Alvinella_pompejana_symbiont	'3833-42 enrichment'	'3838-RT enrichment'	'C08-Guaymas'	'D10-Guaymas'	'847-3-POB 9N'	Candidatus_Arcobacter_sulfidicus	Nautilia_sp._AmH	'846-4-Guaymas'	'C08-POB-9N'	'G08-POB-9N'	'E08-POB-9N'	'D08-POB-9N'	'B08-POB-9N'	'G09-Guyamas'	'F09-Guaymas'	'E09-Guaymas'	'D09-Guaymas'	'C09-Guaymas'	'B10-Guaymas'	'A10-Guaymas'	'D7-Guaymas'	Persephonella_marina	Chlorobium_tepidum	Campylobacter_jejuni	Geobacter_metallireducens
	;
END;

BEGIN CHARACTERS;
	TITLE M1993;
	DIMENSIONS NCHAR=93;
	FORMAT DATATYPE = PROTEIN SYMBOLS = " 1 2 3 4 " MISSING = ? GAP = -  ;
	MATRIX
		Hydrogenobacter_thermophilus           FYAAYPITPATTVGNYIVEDLIRVGGWLYQAEDEIASLGMALGASFAGVKAMTATSGPGLCLMTEFISYAGMTELPIVIVDVQRVGPATGMPT
		Helicobacter_pylori                    FFGGYPITPSSDIMHAMSVALPNCGGHFIQMEDEISGISVSLGASMSGTKSMTASSGPGISLKVEQIGYSFMAEIPLVIADVMRSGPSTGMPT
		Alvinella_pompejana_symbiont           FFGGYPITPSSEVMHTISDLLPKAGGAAIQMEDEIAGVAAAIGAGMSGVRTMTATSGPGISLKAENLGLAQMAEVPLVVVNVMRGGPSTGLPT
		'3833-42 enrichment'                   -SAGYPITPSSEIAHEMSKLLPKVGGVFIQMEDEIAGISVALGASMSGVKSMTNTSGPGISLKAEQIGLAFMAEVPLVITNVMRGGPSTGLPT
		'3838-RT enrichment'                   SFAGYPITPSSEVMHVASYLLPEVGGVAIQMEDEIAGISAAIGASAAGVKSFTATSGPGISLKAEQIGSCFIAEIPLVIVNVMRGGPSTGLPT
		'C08-Guaymas'                          FFAGYPITPASEISELCSQLLPKYGRVFIQMEDEIASIAVAIGASVAGGKAMTATSGPGFSLMQENIGYAVMTEIPVVIVNMMRFGPSTGIPT
		'D10-Guaymas'                          FFAGYPITPSSEVMHTISDLLPKVGGTCIQMEDEIGGICAAIGAAMSGVRSMTATSGPGMSLKAENLGLAQMAEVPLVVVDVMRGGPSTGCPQ
		'847-3-POB 9N'                         FFAGYPITPSSEVAHEMSKLLPKVGGVFIQMEDEIAGISVALGASMSGVKAMTNTSGPGISLKSEQIGLAFMAEVPLVITNVMRGGPSTGLPT
		Candidatus_Arcobacter_sulfidicus       FFAGYPITPSSEVMHVCSDLLPKVGGTSIQMEDEIAGVCATIGASMSGVRSLTATSGPGISLKAENLGLAQMAEVPIVVVNVMRGGPSTGIPT
		Nautilia_sp._AmH                       FFAGYPITPSSEVAHEMSKLLPKVGGQFIQMEDEIAGISVALGASMSGVKSMTNTSGPGISLKAEQIGLAFIAEVPLVITNVMRGGPSTGLPT
		'846-4-Guaymas'                        FFAGYPITPSSEVAHEMSKLLPKVGGQFIQMEDEIAGISVALGASMSGVKSMTNTSGPGISLKSEQIGLAFIAEVPLVITNVMRGGPSTGLPT
		'C08-POB-9N'                           FFAGYPITPSSEVAHELSVLLPRVGGKFIQMEDEIGGICVALGASMSGVKSMTNTSGPGMSLKAEQIGLGFIAEVPLVITNVMRGGPSTGLPT
		'G08-POB-9N'                           FFAGYPITPSSEVMHEISDLLPKVGETCIQMEDEIAAICAVIGAGMAGERTMTGTSGPGMSLKAENLGLAQMAEVPLVCVNVMRGGPSTGLPT
		'E08-POB-9N'                           FFAGYPITPSSEVMHEASDLLPAAGGVAIQMEDEIGGISAALGASMAGVKSFTATSGPGISLKAEQIGLGFIAEIPLVIINVMRGGPSTGLPT
		'D08-POB-9N'                           FFAGYPITPSSEVKHEASDLLPAAGGVAIQMEDEIGGISAALGASMAGVKSFTATSGPGISLKAEQIGLGFIAEIPLVIINVMRGGPSTGLPT
		'B08-POB-9N'                           FFAGYPITPATTVGNYLAPIILKTGGFVYQSEDEISSMAAIIGASFAGAKAMTATSGPGISLMQELIDLASMTELPTVIVDVQRAGPSTGLPT
		'G09-Guyamas'                          FFAGYPITPSSEVAHELSVLLPRNGGKFIQMEDEIAGICVALGASMSGKKAMTNTSGPGISLKAEQIGLGFITEVPMVITNVMRGGPSTGLPT
		'F09-Guaymas'                          FFAGYPITPSTEIAEILSSELPKVGGEFIQMEDEIAAVVAALGASLAGRKSLTASSGPGISLKLENIGFGAMAEIPLVIINVMRGGPSTGLPT
		'E09-Guaymas'                          FFAGYPITPSSEIMHLMAKEMPRVGGVFIQMEDEIASIAAAIGASMAGKIAMTATSGPGFSLMQENIGYAAMAEIPVVIVDVMRVGPSTGLPT
		'D09-Guaymas'                          FFAGYPITPSSEIAEKMAELLPKYGGVFIQMEDEIAAMGATVGGSFAGLKAMTATSGPGFSLKQENLGYAFMVEAPCVVVNVQRGGPSTGLPT
		'C09-Guaymas'                          FFAGYPITPSSEVMHVISDLLPAKGGTAIQMEDEIAGICCVIGAAMSGSRALTATSGPGMSLKAENLGLAQMAEVPLVCVNVMRGGPSTGLPT
		'B10-Guaymas'                          FFAGYPITPSSEIAEKMSELLPKVGGVFIQMEDEIASMAAIVGASFTGAKSMTATSGPGFSLKQENLDYAFFVEAPCVVVNVQRGGPSTGMPT
		'A10-Guaymas'                          FFAGYPITPATEIAEILSDKLPEVGGKFIQMEDEIGSIAATVGASIGGVKSMTATSGPGFSLMQENLGFACITEVPLVLVNVMRGGPSTGLPT
		'D7-Guaymas'                           FFAGYPITPSSEVMHVISDLLPAKGGTAIQMEDEIAGICCVIGAAMSDSRALTATSGPGMSLKAENLGLAQMAEVPLVCVNVMRGGPSTGLPT
		Persephonella_marina                   FFAGYPITPATTVGNYLSPIILKTGGFVYQSEDEISSMAAIIGASFAGVKAMTATSGPGISLMQELIDLASMTELPVVVVDVQRAGPSTGPAP
		Chlorobium_tepidum                     FLGSYPITPASEILQTLAG-LKKWGVKTFQAEDEIAGILTSIGAAYGGALAATNTSGPGLALKTEGMGLAVILELPLVIINVMRGGPSTGLPT
		Campylobacter_jejuni                   FFGGYPITPSSEIAHELSHMLPANDGTFIQMEDEISGISVAIGAAMSGVKSMTASSGPGISLKAEQIGLAFIAEIPLVIVNVMRGGPSTGLPT
		Geobacter_metallireducens              FFAGYPITPSTEVAEVLSAELPKVGGKFMQMEDEIGAMAALIGASLTGSKVLTSTSGPGLSLKQENIGYACIAEVPAVIVNVMRGGPSTGMPT
	;
END;

BEGIN CODONS;
CODESET * UNTITLED = Universal: all ; 
 END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 EXSET * Exclude = 1 20 31 91 93 ; 
 END;