#NEXUS [written Mon Aug 09 17:48:29 BST 2010 by Mesquite version 2.6 (build 486) at casewell-PC/192.168.0.4] BEGIN TAXA; TITLE Echis; DIMENSIONS NTAX=33; TAXLABELS Echis_carinatus_sochureki_02C03_ECS00002 Echis_carinatus_sochureki_13C04_ECS00002 Echis_pyramidum_leakeyi_09E03_EPL00071 Echis_pyramidum_leakeyi_09G08_EPL00071 Echis_pyramidum_leakeyi_10A05_EPL00071 Echis_pyramidum_leakeyi_07H08_EPL00071 Echis_pyramidum_leakeyi_14B06_EPL00071 Echis_pyramidum_leakeyi_08B04_EPL00071 Echis_pyramidum_leakeyi_10H07_EPL00071 Echis_coloratus_05H07_ECO00186 Echis_coloratus_07F07_ECO00086 Echis_coloratus_09D06_ECO00086 Echis_carinatus_sochureki_03F06_ECS00014 Echis_carinatus_sochureki_01H04_ECS00014 Echis_carinatus_sochureki_05A08_ECS00014 Echis_carinatus_sochureki_01G06_ECS00034 Echis_ocellatus_05G03_EOC00015 Echis_pyramidum_leakeyi_13F09_EPL00012 Echis_pyramidum_leakeyi_10H09_EPL00012 Echis_pyramidum_leakeyi_14E11_EPL00012 Echis_pyramidum_leakeyi_14D03_EPL00012 Echis_pyramidum_leakeyi_14D07_EPL00195 Echis_pyramidum_leakeyi_14D04_EPL00012 Echis_pyramidum_leakeyi_01F05_EPL00012 Echis_pyramidum_leakeyi_14G07_EPL00012 Echis_pyramidum_leakeyi_09D09_EPL00195 Echis_coloratus_04H07_ECO00035 Echis_coloratus_01C02_ECO00035 Echis_coloratus_02B02_ECO00035 Echis_pyramidum_leakeyi_06B10_EPL00204 Echis_pyramidum_leakeyi_10D09_EPL00204 Echis_ocellatus_09G11_EOC00079 Homo_sapiens_AB464018_20896703 ; END; BEGIN CHARACTERS; TITLE Echis_phospholipase_A2_amino_acid_alignment; DIMENSIONS NCHAR=144; FORMAT DATATYPE = Protein INTERLEAVE GAP = - MISSING = ?; MATRIX Echis_carinatus_sochureki_02C03_ECS00002 MKT---LWIVAVWLIAVEGNLYQFGRMIWNRTGKPAMFSYGSYGCYCGWGGQGAPQDATDRCCLVHDCCYTRVG--ACSP Echis_carinatus_sochureki_13C04_ECS00002 MKT---LWIVAVWLIAVEGNLYQFGRMIWNRTGKPAMFSYGSYGCYCGWGGQGAPQDATDRCCLVHDCCYTRMG--ACSL Echis_pyramidum_leakeyi_09E03_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSP Echis_pyramidum_leakeyi_09G08_EPL00071 ??????????????????????????????????PAMFSYSAYGCYCGWGGQGKPQDPSDRCCFVHDCCYTRVN--NCSP Echis_pyramidum_leakeyi_10A05_EPL00071 ??T---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSP Echis_pyramidum_leakeyi_07H08_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSP Echis_pyramidum_leakeyi_14B06_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSP Echis_pyramidum_leakeyi_08B04_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFVHDCCYTRVN--NCSP Echis_pyramidum_leakeyi_10H07_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFVHDCCYTRVN--NCSP Echis_coloratus_05H07_ECO00186 MRT---LWIVAVWLMSVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDASDRCCFVHDCCYTRVN--NCSP Echis_coloratus_07F07_ECO00086 MRT---LWIVAVWLMGVEGHLLQFENMIYQKTGKFAIIAYSNYGCYCGWGGKGKPQDATDRCCFVHDCCYGRVN--GCDP Echis_coloratus_09D06_ECO00086 MRT---LWIVAVWLMGVEGHLLQFENMIYQKTGKFAIIAYSNYGCYCGWGGKGKPQDATDRCCFVHDCCYGRVN--GCDP Echis_carinatus_sochureki_03F06_ECS00014 MKT---LWIVAVWLIAVEGSIVELGKMIIQETGKSSFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLP--DCSP Echis_carinatus_sochureki_01H04_ECS00014 MKT---LWIVAVWLIAVEGSIVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLP--DCSP Echis_carinatus_sochureki_05A08_ECS00014 MKT---LWIVAVWLIAVEGSVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLP--DCSP Echis_carinatus_sochureki_01G06_ECS00034 MKT---LWIVAVWLIAFQGSVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLA--DCSP Echis_ocellatus_05G03_EOC00015 MRA---LWIVAVWLIGVEGSVVELGKMIIQETGKSPFPSYTSYGCFCGGGEKGTPKDATDRCCFVHSCCYDKLP--DCSP Echis_pyramidum_leakeyi_13F09_EPL00012 ???????????VWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_10H09_EPL00012 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGRFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_14E11_EPL00012 ??????LWIVAVWLMCVQGSVIQLGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_14D03_EPL00012 MRT---LWIVAVWLMCVQGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_14D07_EPL00195 MRT---LWIVAVWLMCVQGSVIELGKMIIPLTNKTP-ASYVSYGCFCGGGDQGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_14D04_EPL00012 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGQPKDAPDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_01F05_EPL00012 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_14G07_EPL00012 MRT---LWIVALWLMCLEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_09D09_EPL00195 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_coloratus_04H07_ECO00035 MRT---LWIVAVWLMCVEGSVIELGKMIVQLTNKTP-VSYVSYGCFCGGGDRGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_coloratus_01C02_ECO00035 MRT---LWIVAVWLMCVEGSVIELGKMIVQLTNKTP-ASYVSYGCFCGGGDRGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_coloratus_02B02_ECO00035 MRT---LWIVAVWLMCAEGSVIELGKMIVQLTNKTP-ASYVSYGCFCGGGDRGKPKDATDRCCFVHSCCYDTLP--DCSP Echis_pyramidum_leakeyi_06B10_EPL00204 MRT---LLIVAVWLMGVEGSLIEFGKMIFKETGRIPFPFYTSYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLR--DCSP Echis_pyramidum_leakeyi_10D09_EPL00204 MRT---LLIVAVWLMGVEGSLIEFGKMIFKETGRIPFPFYTSYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLR--DCSP Echis_ocellatus_09G11_EOC00079 MRA---LWIVAVWLIGVEGSVIEFGTMIIEETGRSPFPFYTSYGCYCGLGGKGKPKDDTDRCCFVHDCCYGSMP--DCSP Homo_sapiens_AB464018_20896703 MKSPHVLVFLCLLVALVTGNLVQFGVMIEKMTGKSA-LQYNDYGCYCGIGGSHWPVDQTDWCCHAHDCCYGRLEKLGCEP Echis_carinatus_sochureki_02C03_ECS00002 KMTLYSYRFENGDIICDDNDPCKKAVCECDREAAICFGENVNTYDKKYKSY--EHCTEEVQE-C Echis_carinatus_sochureki_13C04_ECS00002 KMTLYSYRFENGDIICDDDDPCKKAVCECDREAAICFGENVNTYDKKYKSY--QHCTEEVQE-C Echis_pyramidum_leakeyi_09E03_EPL00071 KMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEQYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_09G08_EPL00071 KMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEEYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_10A05_EPL00071 KMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTGEETEQC Echis_pyramidum_leakeyi_07H08_EPL00071 KMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_14B06_EPL00071 QMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_08B04_EPL00071 KMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_10H07_EPL00071 KMTLYSYRFENGDIICGDNDPCRKAVCECDRKAAI????????????????????????????? Echis_coloratus_05H07_ECO00186 KMTLYSYRFENEDIICGDDDPCRKAVCECDREAAICLGENVNTYDE?YRFYSSSHC-MEETEQC Echis_coloratus_07F07_ECO00086 KADSYSYSFENGDIVCGDDHPCRRAVCECDRVPTNCFAENLKTYNKKYWLS????????????? Echis_coloratus_09D06_ECO00086 KADSYSYSFENGDIVCGDDDPCRRAVCECDRVAANCFAENLKTYNKKYWLSSIIDCK-EESEKC Echis_carinatus_sochureki_03F06_ECS00014 KTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRKNLNTYNKKYTYYPNFWCK-GDIEKC Echis_carinatus_sochureki_01H04_ECS00014 KTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRKNLNTYNKKYTYYPNFWCK-GDIEKC Echis_carinatus_sochureki_05A08_ECS00014 KTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRKNLNTYNKKYTYYPNFWCK-GDIEKC Echis_carinatus_sochureki_01G06_ECS00034 KTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRNNLNTYNKRYTYYPNFWCK-GDI?KC Echis_ocellatus_05G03_EOC00015 KTDRYKYQRENGEIICENSTSCKKRICECDKAVAVCLRENLQTYNKKYTYYPNFLCK-GEPEKC Echis_pyramidum_leakeyi_13F09_EPL00012 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYKIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_10H09_EPL00012 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14E11_EPL00012 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14D03_EPL00012 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14D07_EPL00195 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDQC Echis_pyramidum_leakeyi_14D04_EPL00012 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_01F05_EPL00012 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14G07_EPL00012 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDHLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_09D09_EPL00195 ITDQYIYK???????????????????????????????????????????????????????? Echis_coloratus_04H07_ECO00035 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRENLKTYNKKYKIYPNILCR-GEPDKC Echis_coloratus_01C02_ECO00035 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRENLKTYNKKYKIYPNILCR-GEPDKC Echis_coloratus_02B02_ECO00035 KTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRENLKTYNKKYKIYPNILCR-GEPDKC Echis_pyramidum_leakeyi_06B10_EPL00204 KTDRYKYHRENGAIVCESGTSCEKRICECDKAAAICFRVNLKTYKNKYMFYPDIFCK-EDTEKC Echis_pyramidum_leakeyi_10D09_EPL00204 KTDRYKYHRENGAIVCESGTSCEKRICECDKPAAIC???????????????????????????? Echis_ocellatus_09G11_EOC00079 KTDIYRYHRENGEIICESGTSCEKRICECDKAAAVCFRENLKTYKNKYMVYPDSLCK-EESEKC Homo_sapiens_AB464018_20896703 KLEKYLFSVSERGIFCAGRTTCQRLTCECDKRAALCFRRNLGTYNRKYAHYPNKLCT-GPTPPC ; END; begin mrbayes; mcmc nruns = 4 ngen = 5000000 nchains = 4 samplefreq = 500 printfreq = 500 savebrlens = yes filename = Echis_ocellatus_PLA2_trans.nex; sumt burnin = 2000 contype = allcompat showtreeprobs = yes filename = Echis_ocellatus_PLA2_trans.nex; END; Begin mrbayes; outgroup Homo_sapiens_AB464018_20896703; set autoclose = yes; begin mrbayes; prset aamodelpr = fixed ( WAG ); lset rates = gamma; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 144; END; BEGIN TREES; Title Echis_phospholipase_A2_amino_acid_tree; LINK Taxa = Echis; TRANSLATE 1 Echis_carinatus_sochureki_02C03_ECS00002, 2 Echis_carinatus_sochureki_13C04_ECS00002, 3 Echis_pyramidum_leakeyi_09E03_EPL00071, 4 Echis_pyramidum_leakeyi_09G08_EPL00071, 5 Echis_pyramidum_leakeyi_10A05_EPL00071, 6 Echis_pyramidum_leakeyi_07H08_EPL00071, 7 Echis_pyramidum_leakeyi_14B06_EPL00071, 8 Echis_pyramidum_leakeyi_08B04_EPL00071, 9 Echis_pyramidum_leakeyi_10H07_EPL00071, 10 Echis_coloratus_05H07_ECO00186, 11 Echis_coloratus_07F07_ECO00086, 12 Echis_coloratus_09D06_ECO00086, 13 Echis_carinatus_sochureki_03F06_ECS00014, 14 Echis_carinatus_sochureki_01H04_ECS00014, 15 Echis_carinatus_sochureki_05A08_ECS00014, 16 Echis_carinatus_sochureki_01G06_ECS00034, 17 Echis_ocellatus_05G03_EOC00015, 18 Echis_pyramidum_leakeyi_13F09_EPL00012, 19 Echis_pyramidum_leakeyi_10H09_EPL00012, 20 Echis_pyramidum_leakeyi_14E11_EPL00012, 21 Echis_pyramidum_leakeyi_14D03_EPL00012, 22 Echis_pyramidum_leakeyi_14D07_EPL00195, 23 Echis_pyramidum_leakeyi_14D04_EPL00012, 24 Echis_pyramidum_leakeyi_01F05_EPL00012, 25 Echis_pyramidum_leakeyi_14G07_EPL00012, 26 Echis_pyramidum_leakeyi_09D09_EPL00195, 27 Echis_coloratus_04H07_ECO00035, 28 Echis_coloratus_01C02_ECO00035, 29 Echis_coloratus_02B02_ECO00035, 30 Echis_pyramidum_leakeyi_06B10_EPL00204, 31 Echis_pyramidum_leakeyi_10D09_EPL00204, 32 Echis_ocellatus_09G11_EOC00079, 33 Homo_sapiens_AB464018_20896703; TREE con_all_compat = (33:0.97879,(((1:0.013815,2:0.034002)1.00:0.16553,((((3:0.01513,((5:0.015526,6:0.007594)0.20:0.007547,7:0.015048)0.20:0.007752)0.98:0.015079,8:0.007598)0.23:0.007858,(4:0.017612,9:0.020098)0.28:0.011087)0.97:0.026708,10:0.035624)1.00:0.059327)1.00:0.179034,(11:0.035984,12:0.009504)1.00:0.234616)1.00:0.226081,(((((13:0.015806,14:0.007906)0.90:0.015251,(15:0.007873,16:0.047879)0.34:0.009323)1.00:0.113498,((18:0.009967,((((19:0.015661,24:0.007829)0.11:0.0079,(((20:0.016027,21:0.007846)0.34:0.008477,22:0.031992)0.94:0.015583,23:0.023627)0.11:0.008127)0.06:0.007967,25:0.031746)0.27:0.014038,26:0.039822)0.37:0.014465)0.53:0.027221,(27:0.015447,(28:0.007754,29:0.015606)0.33:0.007937)0.98:0.046086)1.00:0.147875)0.49:0.035702,17:0.0375)1.00:0.150756,((30:0.011022,31:0.020143)1.00:0.134726,32:0.12621)0.99:0.095689)1.00:0.220481); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 144; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 144; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8739275604876138401; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2139565914243781577; checksumv 0 2 459817455 null; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; endTell; end;