#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; 20:58 GMT TreeBASE (cc) 1994-2008 Study reference: Casewell N.R., Wagstaff S.C., Harrison R.A., & Wuster W. 2010. Gene tree parsimony of multi-locus snake venom protein families reveals species tree conflict as a result of multiple parallel gene loss. Molecular Biology and Evolution, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10791] [ The following blocks are input data for analysis step 6339 ] BEGIN TAXA; TITLE TaxaForAnalysisStep6339; DIMENSIONS NTAX=33; TAXLABELS Echis_carinatus_sochureki_01G06_ECS00034 Echis_carinatus_sochureki_01H04_ECS00014 Echis_carinatus_sochureki_02C03_ECS00002 Echis_carinatus_sochureki_03F06_ECS00014 Echis_carinatus_sochureki_05A08_ECS00014 Echis_carinatus_sochureki_13C04_ECS00002 Echis_coloratus_01C02_ECO00035 Echis_coloratus_02B02_ECO00035 Echis_coloratus_04H07_ECO00035 Echis_coloratus_05H07_ECO00186 Echis_coloratus_07F07_ECO00086 Echis_coloratus_09D06_ECO00086 Echis_ocellatus_05G03_EOC00015 Echis_ocellatus_09G11_EOC00079 Echis_pyramidum_leakeyi_01F05_EPL00012 Echis_pyramidum_leakeyi_06B10_EPL00204 Echis_pyramidum_leakeyi_07H08_EPL00071 Echis_pyramidum_leakeyi_08B04_EPL00071 Echis_pyramidum_leakeyi_09D09_EPL00195 Echis_pyramidum_leakeyi_09E03_EPL00071 Echis_pyramidum_leakeyi_09G08_EPL00071 Echis_pyramidum_leakeyi_10A05_EPL00071 Echis_pyramidum_leakeyi_10D09_EPL00204 Echis_pyramidum_leakeyi_10H07_EPL00071 Echis_pyramidum_leakeyi_10H09_EPL00012 Echis_pyramidum_leakeyi_13F09_EPL00012 Echis_pyramidum_leakeyi_14B06_EPL00071 Echis_pyramidum_leakeyi_14D03_EPL00012 Echis_pyramidum_leakeyi_14D04_EPL00012 Echis_pyramidum_leakeyi_14D07_EPL00195 Echis_pyramidum_leakeyi_14E11_EPL00012 Echis_pyramidum_leakeyi_14G07_EPL00012 Homo_sapiens_AB464018_20896703 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M6391] TITLE Echis_phospholipase_A2_amino_acid_alignment; LINK TAXA = TaxaForAnalysisStep6339; DIMENSIONS NCHAR=144; 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 ] [ . . . . . . . . . . . . . . ] Echis_carinatus_sochureki_01G06_ECS00034 MKT---LWIVAVWLIAFQGSVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLA--DCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRNNLNTYNKRYTYYPNFWCK-GDI?KC Echis_carinatus_sochureki_01H04_ECS00014 MKT---LWIVAVWLIAVEGSIVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLP--DCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRKNLNTYNKKYTYYPNFWCK-GDIEKC Echis_carinatus_sochureki_02C03_ECS00002 MKT---LWIVAVWLIAVEGNLYQFGRMIWNRTGKPAMFSYGSYGCYCGWGGQGAPQDATDRCCLVHDCCYTRVG--ACSPKMTLYSYRFENGDIICDDNDPCKKAVCECDREAAICFGENVNTYDKKYKSY--EHCTEEVQE-C Echis_carinatus_sochureki_03F06_ECS00014 MKT---LWIVAVWLIAVEGSIVELGKMIIQETGKSSFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLP--DCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRKNLNTYNKKYTYYPNFWCK-GDIEKC Echis_carinatus_sochureki_05A08_ECS00014 MKT---LWIVAVWLIAVEGSVVELGKMIIQETGKSPFPSYTSYGCFCGGGERGPPLDATDRCCLAHSCCYDTLP--DCSPKTDRYKYKRENGEIICENSTSCKKRICECDKAMAVCLRKNLNTYNKKYTYYPNFWCK-GDIEKC Echis_carinatus_sochureki_13C04_ECS00002 MKT---LWIVAVWLIAVEGNLYQFGRMIWNRTGKPAMFSYGSYGCYCGWGGQGAPQDATDRCCLVHDCCYTRMG--ACSLKMTLYSYRFENGDIICDDDDPCKKAVCECDREAAICFGENVNTYDKKYKSY--QHCTEEVQE-C Echis_coloratus_01C02_ECO00035 MRT---LWIVAVWLMCVEGSVIELGKMIVQLTNKTP-ASYVSYGCFCGGGDRGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRENLKTYNKKYKIYPNILCR-GEPDKC Echis_coloratus_02B02_ECO00035 MRT---LWIVAVWLMCAEGSVIELGKMIVQLTNKTP-ASYVSYGCFCGGGDRGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRENLKTYNKKYKIYPNILCR-GEPDKC Echis_coloratus_04H07_ECO00035 MRT---LWIVAVWLMCVEGSVIELGKMIVQLTNKTP-VSYVSYGCFCGGGDRGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRENLKTYNKKYKIYPNILCR-GEPDKC Echis_coloratus_05H07_ECO00186 MRT---LWIVAVWLMSVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDASDRCCFVHDCCYTRVN--NCSPKMTLYSYRFENEDIICGDDDPCRKAVCECDREAAICLGENVNTYDE?YRFYSSSHC-MEETEQC Echis_coloratus_07F07_ECO00086 MRT---LWIVAVWLMGVEGHLLQFENMIYQKTGKFAIIAYSNYGCYCGWGGKGKPQDATDRCCFVHDCCYGRVN--GCDPKADSYSYSFENGDIVCGDDHPCRRAVCECDRVPTNCFAENLKTYNKKYWLS????????????? Echis_coloratus_09D06_ECO00086 MRT---LWIVAVWLMGVEGHLLQFENMIYQKTGKFAIIAYSNYGCYCGWGGKGKPQDATDRCCFVHDCCYGRVN--GCDPKADSYSYSFENGDIVCGDDDPCRRAVCECDRVAANCFAENLKTYNKKYWLSSIIDCK-EESEKC Echis_ocellatus_05G03_EOC00015 MRA---LWIVAVWLIGVEGSVVELGKMIIQETGKSPFPSYTSYGCFCGGGEKGTPKDATDRCCFVHSCCYDKLP--DCSPKTDRYKYQRENGEIICENSTSCKKRICECDKAVAVCLRENLQTYNKKYTYYPNFLCK-GEPEKC Echis_ocellatus_09G11_EOC00079 MRA---LWIVAVWLIGVEGSVIEFGTMIIEETGRSPFPFYTSYGCYCGLGGKGKPKDDTDRCCFVHDCCYGSMP--DCSPKTDIYRYHRENGEIICESGTSCEKRICECDKAAAVCFRENLKTYKNKYMVYPDSLCK-EESEKC Echis_pyramidum_leakeyi_01F05_EPL00012 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_06B10_EPL00204 MRT---LLIVAVWLMGVEGSLIEFGKMIFKETGRIPFPFYTSYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLR--DCSPKTDRYKYHRENGAIVCESGTSCEKRICECDKAAAICFRVNLKTYKNKYMFYPDIFCK-EDTEKC Echis_pyramidum_leakeyi_07H08_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSPKMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_08B04_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFVHDCCYTRVN--NCSPKMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_09D09_EPL00195 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSPITDQYIYK???????????????????????????????????????????????????????? Echis_pyramidum_leakeyi_09E03_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSPKMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEQYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_09G08_EPL00071 ??????????????????????????????????PAMFSYSAYGCYCGWGGQGKPQDPSDRCCFVHDCCYTRVN--NCSPKMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEEYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_10A05_EPL00071 ??T---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSPKMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTGEETEQC Echis_pyramidum_leakeyi_10D09_EPL00204 MRT---LLIVAVWLMGVEGSLIEFGKMIFKETGRIPFPFYTSYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLR--DCSPKTDRYKYHRENGAIVCESGTSCEKRICECDKPAAIC???????????????????????????? Echis_pyramidum_leakeyi_10H07_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFVHDCCYTRVN--NCSPKMTLYSYRFENGDIICGDNDPCRKAVCECDRKAAI????????????????????????????? Echis_pyramidum_leakeyi_10H09_EPL00012 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGRFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_13F09_EPL00012 ???????????VWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYKIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14B06_EPL00071 MRT---LWIVAVWLMGVEGNLYQFGKMIKNKTGKPAMFSYSAYGCYCGWGGQGKPQDPSDRCCFMHDCCYTRVN--NCSPQMTLYSYRFENGDIICGDNDPCRKAVCECDREAAICLGENVNTYDEKYRFYSSSYCTEEETEQC Echis_pyramidum_leakeyi_14D03_EPL00012 MRT---LWIVAVWLMCVQGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14D04_EPL00012 MRT---LWIVAVWLMCVEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGQPKDAPDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14D07_EPL00195 MRT---LWIVAVWLMCVQGSVIELGKMIIPLTNKTP-ASYVSYGCFCGGGDQGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDQC Echis_pyramidum_leakeyi_14E11_EPL00012 ??????LWIVAVWLMCVQGSVIQLGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDNLNTYNKKYRIYPNFLCR-GDPDKC Echis_pyramidum_leakeyi_14G07_EPL00012 MRT---LWIVALWLMCLEGSVIELGKMIIQLTNKTP-ASYVSYGCFCGGGDKGKPKDATDRCCFVHSCCYDTLP--DCSPKTDQYKYKWENGEIICENSTSCKKRICECDKAVAICLRDHLNTYNKKYRIYPNFLCR-GDPDKC Homo_sapiens_AB464018_20896703 MKSPHVLVFLCLLVALVTGNLVQFGVMIEKMTGKSA-LQYNDYGCYCGIGGSHWPVDQTDWCCHAHDCCYGRLEKLGCEPKLEKYLFSVSERGIFCAGRTTCQRLTCECDKRAALCFRRNLGTYNRKYAHYPNKLCT-GPTPPC ; END; [ The following blocks are output data for analysis step 6339 ] BEGIN TREES; TITLE Echis_phospholipase_A2_amino_acid_TB; LINK TAXA = TaxaForAnalysisStep6339; TREE Echis_PLA2_AA = [&R] (Homo_sapiens_AB464018_20896703:0.97879,(((Echis_carinatus_sochureki_02C03_ECS00002:0.013815,Echis_carinatus_sochureki_13C04_ECS00002:0.034002)1.00:0.16553,((((Echis_pyramidum_leakeyi_09E03_EPL00071:0.01513,((Echis_pyramidum_leakeyi_10A05_EPL00071:0.015526,Echis_pyramidum_leakeyi_07H08_EPL00071:0.007594)0.20:0.007547,Echis_pyramidum_leakeyi_14B06_EPL00071:0.015048)0.20:0.007752)0.98:0.015079,Echis_pyramidum_leakeyi_08B04_EPL00071:0.007598)0.23:0.007858,(Echis_pyramidum_leakeyi_09G08_EPL00071:0.017612,Echis_pyramidum_leakeyi_10H07_EPL00071:0.020098)0.28:0.011087)0.97:0.026708,Echis_coloratus_05H07_ECO00186:0.035624)1.00:0.059327)1.00:0.179034,(Echis_coloratus_07F07_ECO00086:0.035984,Echis_coloratus_09D06_ECO00086:0.009504)1.00:0.234616)1.00:0.226081,(((((Echis_carinatus_sochureki_03F06_ECS00014:0.015806,Echis_carinatus_sochureki_01H04_ECS00014:0.007906)0.90:0.015251,(Echis_carinatus_sochureki_05A08_ECS00014:0.007873,Echis_carinatus_sochureki_01G06_ECS00034:0.047879)0.34:0.009323)1.00:0.113498,((Echis_pyramidum_leakeyi_13F09_EPL00012:0.009967,((((Echis_pyramidum_leakeyi_10H09_EPL00012:0.015661,Echis_pyramidum_leakeyi_01F05_EPL00012:0.007829)0.11:0.0079,(((Echis_pyramidum_leakeyi_14E11_EPL00012:0.016027,Echis_pyramidum_leakeyi_14D03_EPL00012:0.007846)0.34:0.008477,Echis_pyramidum_leakeyi_14D07_EPL00195:0.031992)0.94:0.015583,Echis_pyramidum_leakeyi_14D04_EPL00012:0.023627)0.11:0.008127)0.06:0.007967,Echis_pyramidum_leakeyi_14G07_EPL00012:0.031746)0.27:0.014038,Echis_pyramidum_leakeyi_09D09_EPL00195:0.039822)0.37:0.014465)0.53:0.027221,(Echis_coloratus_04H07_ECO00035:0.015447,(Echis_coloratus_01C02_ECO00035:0.007754,Echis_coloratus_02B02_ECO00035:0.015606)0.33:0.007937)0.98:0.046086)1.00:0.147875)0.49:0.035702,Echis_ocellatus_05G03_EOC00015:0.0375)1.00:0.150756,((Echis_pyramidum_leakeyi_06B10_EPL00204:0.011022,Echis_pyramidum_leakeyi_10D09_EPL00204:0.020143)1.00:0.134726,Echis_ocellatus_09G11_EOC00079:0.12621)0.99:0.095689)1.00:0.220481); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr21100] END;