#NEXUS [written Thu Aug 21 00:16:41 EDT 2014 by Mesquite version 2.75 (build 564) at owner-PC/10.0.0.5] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=43; TAXLABELS Cadophora_finlandica_AF486119 Mycelium_radicis_atrovirens_AF486120 Phialocephala_dimorphospora_AF486121 Phialocephala_fusca_AF486122 Sporendocladia_bactrospora_AF486123 Phialocephala_fluminis_AF486124 Phialocephala_compacta_AF486125 Phialocephala_scopiformis_AF486126 Kendrickiella_phycomyces_AF486127 Phialocephala_xalapensis_AF486128 Sporendocladia_foliicola_AF486129 Sporendocladia_bactrospora_AF486130 Phialocephala_humicola_AF486131 Phialocephala_virens_AF486132 Leptodontidium_orchidicola_AF486133 Phialocephala_turiciensis_AY078128 Phialocephala_turiciensis_AY078129 Phialocephala_letzii_AY078130 Phialocephala_cf._fortinii_AY078131 Phialocephala_cf._fortinii_AY078132 Phialocephala_europaea_AY078133 Phialocephala_fortinii_AY078134 Phialocephala_fortinii_AY078135 Phialocephala_helvetica_AY078136 Phialocephala_europaea_AY078137 Phialocephala_fortinii_AY078138 Phialocephala_fortinii_AY078139 Phialocephala_fortinii_AY078140 Phialocephala_fortinii_AY078141 Phialocephala_helvetica_AY078142 Phialocephala_fortinii_AY078143 Phialocephala_fortinii_AY078144 Acephala_applanata_AY078145 Acephala_applanata_AY078146 Acephala_applanata_AY078147 Acephala_applanata_AY078148 Acephala_applanata_AY078149 Acephala_applanata_AY078150 Acephala_applanata_AY078151 Phialocephala_cf._fortinii_AY078152 Sclerotinia_sclerotiorum_NW_001820801 Phialocephala_fortinii_PPE5ITS Phialocephala_podophyllae_PPE7ITS ; END; BEGIN CHARACTERS; TITLE PPE5&7_ITS_alignment; DIMENSIONS NCHAR=478; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Cadophora_finlandica_AF486119 ?????????????????????????????????????????????????????????????????AACAADBCBBBBCDDDDDDCAAA------DCCCDDBDADDB-BBAAABBC--DCDADABA-DABBDDDC--DDCBDDDCCBACCBBCBB-----DDDDACC------BCDBCCBDBBCCBDCABD----------CBCBBDCBBACACC----AB--BBAAABDBDDDDC--DDDACDCADCDBDCA--CDABDADADAADA--CDDA--------DAABBABDBAACBBDBCCBDDC-CDBDDCCCCDDBCB---CCDDDB------CBCCBBBDDAAAADBACDCCBCCDCBBC--DBDCCBDBD--AACBCDACDA-ADDB------DBDBCBDADACCCDBBACCDCABB-ABBDCBBAD---AABBBBBAD-----DBDDDAB????????????????????????? Mycelium_radicis_atrovirens_AF486120 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCBABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDA-CBDBCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Phialocephala_dimorphospora_AF486121 ????????????????????????????????????????????????????ADBACDCCADBBCCBCCCCCABDBCDAAAACACCADB--BBBCDBCCCDACABB-DBBABBBC--DCBBDABB-DABDBDDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDABCCCBDBDCBDBCDAB---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--ADDACDCADCDBDCA--CAABDADDDAADA--CDDA--------ACABBABDBABCB-BDCCBCDC-CDADDCCCCBABCB---CCDDBB------CBCCBBBDBAAAADBACDCCBCCBCBBC--CDACCBBBD--AACBCDACDAAADBD------DBDBCBDADACCCDBBDBDBCCDC-CBDBCBBAC---AABBBBBAA-----BDDBDBAA???????????????????????? Phialocephala_fusca_AF486122 ?????????????????????????????????????????????????????????????????????????????????????????????????????AACCAABDBCBAAC---ABDBBDAABBBABD---CDCAABBDABBBCA-BCDD-----CBBDBCC-BCCCBCBBBCCBBDBCBCBBCCCBABBAAC--BBBCBBCCB--CCB--BBBBDABDBDCDBDBDC-BACBCDDC-DCDBDBBCA---CDADABBAAAABAA-CDBA--------BBABBB-DBACCB-CBDCBBDC-CDCDDCCCCCBBDC---BCBB-DC-----BACBBDBBCAAACBBAABCCBCCDBBBCCDBBBCCBBBB--CACBCDACDACB-ADA-----BBDBCBDBDCCCBCBBDCCBCCCBA-BBACBBCBA--AB-BBABBA-----DBDBAACCDDCABBDBCCADBACBDA?????? Sporendocladia_bactrospora_AF486123 ???????????????????????????????????????????????????????????????????????????????????????????????????????DBCACDDABBD----ABDBADDABABBBDDADCDCAABBDABBCACDBCDD-----CBCDBCC-BCCCDCBBCCCADDBCBBBBCBCBBDCBBCCDBDBCBACBBDBACAAABDBDDBDDDACDBDDDACDACDAADDAAADCBDCACDCBAAABABABAAABA--CDBA--------BAABB-BDBAACB-DBBCBDDC-CDCDDCCCAACDBBBCDCBBDBCCBCBCBCCCABBBBBCAAADCAACDCCCBDCDBBBAABBCABABABBDDCBCDACDAAACDBDBDDDCDBDBCBAABCCBCBCBCCADCCBC-CBAACBBCDD--AABBDABADABADADDDDDDDCDCCDDCABBDBCAADBACCDACCA Phialocephala_fluminis_AF486124 ??????????????????????????????????????????????????????????????????????????BBCACDDACCCDDCBBDBDDBCCBCBBBCABBDBBBAABBBDDDCBBDADDADABBDDCDBCDDCBDDBCCBCCABBCCDBDDCABBBDBDBCCCCCBBDBCABBCBBCCCCDBBABBBBDCCACACBCDBBCBBCABCCBBBAABBABAAABDBDDCDABBAAABBADCDBCDBDCA--ADADDBDDCADDAAAADBAAAAABA--DBBDBBBDBAAABBDBCCCDDDCCDCDDCCABBCACDDCBCAADDDDCAABAABDCCDBDBAAACABAADCABCCBCDBB--CDCCCABBBD-BCCDCBAABCACBDDDDACCACBABCBCDBCACDBDAAACCABBBDBBCCCBBCCDBDAABBBDDDD---DABDDBDAA????????????????????????? Phialocephala_compacta_AF486125 ??????????????????????????????????????????????????????BAACDCAACBCCDBCACBABDBCACACACDCADD------ACCBDCBDDABA-BBBABBBC--DCDBDABA-DABDBDDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDABCCCBDBDCBDBCBCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDAABCDBDCA--CDADDADDDAADA--CDDA---------CABBABDBAACB-BBACBDDC-CDCDDCCCCBABCB---CCBDBB------CBCCBBBDDAAACABACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBCC---AABBBBBAA----DBDDDDABA???????????????????????? Phialocephala_scopiformis_AF486126 ??????????????????????????????????????????????????????ADAACCADCBDCCAACCCCCDCACBDBABCBBDBB--BBDACABCCDADABB--BBABBBC--DCDBDADB-DABDBDDC--DDCBDDDCCBACCBBCDC-----CBBDBBA------BDCDCCCBDBDCBBDCBAD---------CDCBBDCBBACACC----AD--D-AAABDBDCAAD--DDDACDCADCDBDCA--CAABDADBDAADA--CDDA--------DAABBABDBAACB-BDCCBDDC-CDCDDCCCCDDDCB---CCDDBB------CBACBBBBDAAAADBACDCCBCCDCBBC--CDCCCBDBD--ABCBCDACDAAADBD------BBDBCBCADDCACDDBBBBBCCDC-CBBDCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Kendrickiella_phycomyces_AF486127 ??????????????????????????????????????????????????????????????????????????BBCACDCACCCB-----BBDBDCCCDBBAABBDBBBA--BBBCDCDDDADD-DABBDDCD---DCBDDBCCBCACBBDCBBDDDDCCBDCBBCCCCCABCDBACDBBBBCCCDBB-----------CDCBDBCBBCCACAB---ABBDDACAABDBDCD-BDCAACADDCDACDBDCA--CADDAA---ADADAAADDADDDA----BDCBB-BDBAACB-ABCCBDDCDCDCDDCCCBBBBCDBBDBBDDBBCCCCC-ABCCCDBBCAAACCBACBCCBCCBABBCBCDBBCCDBBDB-AACBCDADCCCCBDDDCDB--ABDBCBDDDCDACCBBDCCBBCCB-CBDDCBBCAD--BAABBAAAB-----DDDDDADBAACCDDCABBDBCCAD???????? Phialocephala_xalapensis_AF486128 ??????????????????????????????????????????????????????????????????????????????????????????????????????BACCABDBCBAAC---ABDBBDDABABBBD---CDCAABBDDABDC-------------------DADABCBCDDCBDDBCC--BCCCDBB---C--BBBCBBCCB--ACBADABBABADDBDCDDDBD--BDCBCDDCCBADBDBCAC---AAAAAACBAAADAA-CDDA--------BAABBBBDBACCB-BBDCBBDC-CBCDDCCACCABDC---BCBDABC-----BACBBDBBBAAACBAACBCCBCCBCCBC-BBBBAAADBB--CAABCBACDACDDABB-----DBDBCDDBDCCCDCBDCCCABCCBCDBBCCBBCCA--AAABBBBBA-----DBDADADBCD?????????????????????? Sporendocladia_foliicola_AF486129 ??????????????????????????????????????????????????????????????????????????BACACDDBADCBBBD-----DABCCCDACADBDBBBABBBD-ADCD-DADDADAB-DADC--DDCBDDDCCBACCBBCBB------DBDBCA---CCBDABBCCBDBBCCBDCCDCB---------CDCBBDCBBACACA----AB-BBBAAABDBDCAA---ADDACDCDDCDBDCA--CDABDADADAADAA-CDDA---------AABB-DDBAADB-DBDCBDDC-C????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? Sporendocladia_bactrospora_AF486130 ???????????????????????????????????????????????????????????????????????????????????????????????????????DBCACDDABBD----ABDBADDABABBBDDADCDCAABBDABBCACDBCDD-----CBCDBCC-BCCCDCBBCCCADDBCDBBBCBCBBDCBBCCDBDBCBACBBDBACAAABDBDDBDDDACDBDDDACDACDAADDAAADCBDCACDCBAAABABABAAABA--CDBA--------BAABB-BDBAACB-DBBCBDDC-CDCDDCCCAACDBBBCDCBBDBCCBCBCBCCCABBBBBCAAADCAACDCCCBDCDBBBAABBCABABABBDDCBCDACDAAACDBDBDDDCDBDBCBAABCCBCBCBCCADCCBC-CBAACBBCDD--AABBDABADABADADDDDDDDCD??????????????????????? Phialocephala_humicola_AF486131 ??????????????????????????????????????????????????????????????????????????????????????????????????????BACCABDBCBAAC---ABDBBDDABABBBD---CDCAABBDDABDC-------------------DADABCBCDDCBDDBCC--BCCCDBB---C--BBBCBBCCB--ACBADABBABADDBDCDDDBD--BDCBCDDCCBADBDBCAC---AAAAAACBAAADAA-CDDA--------BAABBBBDBACCB-BBDCBBDC-CBCDDCCACCABDC---BCBDABC-----BACBBDBBBAAACBAACBCCBCCBCCBC-BBBBAAADBB--CAABCBACDACDDABB-----DBDBCDDBDCCCDCBDCCCABCCBCDBBCCBBCCA--AAABBBBBA-----DBDADADBCD?????????????????????? Phialocephala_virens_AF486132 ??????????????????????????????????????????????????????????????????????????BACACDDBADCBBBD-----DBCCCCDACABBDBBBABBBDDCDCDADDDDADABBDDDC--DDCBDDDCCBACCBBCBCAC---CBDDBCCBBBBCBDABBCCBBBBCCBDCCDAB---------CDCBBDCBBACACC----BB-BBBAAABDBDCAADD-ADDACDCDBCDBDCA--CDABDADADAADA--CDDA-------ABAABB-BDBAACB-DBDCBDDC-CDADDCCCABDBCBDCBCCAACBC-----CBCCABBDDAAAADBACDCCBCCDCBBA--DBDCCBDBD--AACBCDACDAADABD------DBDBCBDADACCCDBBBCCDCCAD-CBBDCBBACB--AABBBBDAA----DDDDBDAD????????????????????????? Leptodontidium_orchidicola_AF486133 BDACACBAAACCADACABACBCBBBCBCCACBDBCBDBBBCCCCBDABBBDABDBBBCDACCCDDDACACDBCDBCCCBBDBDBCCACA--ACBDBCCDBBDCAAB-DBBABBBD--DCAADAAABDABBDDDC--DDCBDDDCCBCCCBBCBB-----DBCD-CB------BACBCCBDDBCCBDCDDCA---------CDCBBBCBBACACC----AB--BBBAABDBDDCDD--DDDACDCADCDBDCA--CDABDADADAADA--CDDA--------DAABBABDBAACBDBDBCBDDC-CDADDCCCCDDBCB---CCDDDB------CBCCBBBBDAAAADBACDCCBCCDCBBD--CDBCCBDBD--ABCBCDACDAADABD------BBDBCBCADDCACDBBCCDACCDBDABDDCBBACB--AABBBBDAA-----DDDDDDDAA??????????????????????? Phialocephala_turiciensis_AY078128 ??????????????????????????????????????????????????????BAACDCACCBD-BBCAABCBDCCAAABACBCCDB------CCCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCD---CCDBDB------CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBDBBAA----DDDDDDABA???????????????????????? Phialocephala_turiciensis_AY078129 ??????????????????????????????????????????????????????BAACDCACCBD-BBCAABCBDCCAAABAABCCDB------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDB------CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBDBBAA----DDDDDDABA???????????????????????? Phialocephala_letzii_AY078130 ??????????????????????????????????????????????????????BAACDCACCDDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDA-CDADDCCCCBABCB---CCDBDB------CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDDDABA?????????????????????? Phialocephala_cf._fortinii_AY078131 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCBABCB---CCDBDBB-----CBCCBBBDBAAAADDACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Phialocephala_cf._fortinii_AY078132 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBAACB-BDACBDDC-CDADDCCCCBABCB---CCDBDDB-----CBCCBBBDBAAAADDACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CDDDCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Phialocephala_europaea_AY078133 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABADDCCAAABACBDCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-DDACBCDC-CDADDCCACBABCB---CCDBDB------CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDDBDBBCCDC-CBDBCBBAC---AABBBBAA--------DDDDDABA?????????????????????? Phialocephala_fortinii_AY078134 ??????????????????????????????????????????????????????BAACDCACCCDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDBB-----CBCCBBBDBAAAADCACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Phialocephala_fortinii_AY078135 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDABCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCBABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBDCCDC-CBDCCBBAC---AABBBBBAA-----DDDDDABACC?????????????????????? Phialocephala_helvetica_AY078136 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABBBDCAAD--CDDACDCADCDBACA--CDABDADDDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDB------CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Phialocephala_europaea_AY078137 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDB------CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDDBDBBCCDC-CBDBCDBAC---AABBBBBAAADDDDDDDDDDDABA?????????????????????? Phialocephala_fortinii_AY078138 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDBB-----CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDBBBBBBCCDC-CBDBCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Phialocephala_fortinii_AY078139 ??????????????????????????????????????????????????????BAACDCACCBD-BBAAABCBDCCAAABACBCCDB------ACCA-CBDDABA-BBBABBBC--DCDBDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCBABCB---CCDBDBB-----CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDDD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA-----DDDDDABACC?????????????????????? Phialocephala_fortinii_AY078140 ??????????????????????????????????????????????????????BCACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDBDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDBB-----CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Phialocephala_fortinii_AY078141 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBCBCB---CCDBDB------CBCCBBBDBAAAADDACDACBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDD-ABA?????????????????????? Phialocephala_helvetica_AY078142 ??????????????????????????????????????????????????????BBACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDB------CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDDBDBBCCDC-CBDBCDBAC---AABBBBBAA--DDDDDDDDDDABA?????????????????????? Phialocephala_fortinii_AY078143 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCACD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDBB-----CBCCBBBDBAAAADDACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Phialocephala_fortinii_AY078144 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCDDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABBADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACA----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDACBCDC-CDADDCCCCBABCB---CCDBDBB-----BBCCBBBDBAAAADCACDCCBCCBCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA-----DDDDDABA???????????????????????? Acephala_applanata_AY078145 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----ABBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCDABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Acephala_applanata_AY078146 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----ABBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA------DDDAABBABDBABCB-BDCCBCDC-CDADDCCCCDABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Acephala_applanata_AY078147 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----ABBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCDABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Acephala_applanata_AY078148 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----ABBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCDABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Acephala_applanata_AY078149 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----ABBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCDABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Acephala_applanata_AY078150 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----ABBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA------DDDAABBABDBABCB-BDCCBCDC-CDADDCCCCDABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Acephala_applanata_AY078151 ??????????????????????????????????????????????????????BAACDCACCBDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----ABBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCBBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBABCB-BDCCBCDC-CDADDCCCCDABCB---CCDBDB------CBCCBBBDBAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDBCBBAC---AABBBBBAA----DDDDDDABA???????????????????????? Phialocephala_cf._fortinii_AY078152 ??????????????????????????????????????????????????????BAACDCACCDDABBCAABCBDCCAAABACBCCDD------ACCA-CBDDABA-BBBABBBC--DCDDDABA-DABDADDC--DDCBDDDCCBCCCBBCDC-----CBBDBBA------BDCBCCCBDBDCBDBCDCD---------CDCDBBCBBACACC----AB--B-AAABDBDCAAD--CDDACDCADCDBDCA--CDABDADBDAADA--CDDA---------AABBABDBAACB-BDACBDDC-CDADDCCCCBABCB---CCDBD-B-----CBCCBBBDBAAAADDACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDABADAB------DBBBCBDADACACDDBBBBBCCDC-CBDDCDBAC---AABBBBBAA-----DDDDDABA???????????????????????? Sclerotinia_sclerotiorum_NW_001820801 ??????????????????????????????????????????????????????????????????????????BACACDDBADCBBBC-----AAACCCDACABBDBBBABBBD--DCDCDADDADDABDDDC--DDCBDDDCCBCACBDCBD------------------BDDBCCCCBBD-----DCD---------ADCBDBCBBACACA----ADADBAAAABDBDDDDD--ADDAADCDBCDBDCA--CDABDADADAADA--CDDA--------BAABB-BDBAACB-DBACBDDC-CDADDCAC-DBBADCDBACDAADC-----CBACCBDBDAAAADBACDCCBCCBCBBC--BDCCCDBBD--CAABCDACDAADADB------DBDBCDDABAC-CDDBDBCCDCDCBDDBDCBBAA---AABBBAAAD-----DDDBDAD????????????????????????? Phialocephala_fortinii_PPE5ITS ??????????????????????????????????????????????????????????????????????????BBCACDCACCCB-----BBDBDCCCDBBAABBDBBBA--BBBCDCDDDADBCDABBDDCD---DCBDDBCCBCCCBBBCBBCBAACCBDCBBCCCCCCBADBDCBBBDBDCCBBB-----------CBCBBBCBBCAACAB---ABBADDCAABCBDCD-BDCAACADDCBACDBDCA--CBAADD---ACDDAAADAABDDA----BDCBB-BDBAACB-ABCCBDDCDCDCDDCCCBDBBCDBBDBBDDBBCCCCC-ABCCCBBBCAAACCBACBCCBCCBABBCBCDBBCCDBBDB-CACBCDADCCCCBDDBCDB--ABBBCBDBDCDACCBBBCCBBCCB-CBDDCBBCAB--ABADBAADB-----DDDDDDBBA??????????????????????? Phialocephala_podophyllae_PPE7ITS ???????????????????????????????????????????????????????????????????????????AAAACCADABBCCC--A--AABBCCDACABB--BAABBBC--DCDBDADD-DABDBDDC--DDCBDDDCCBACCBBCDC-----CBBDBBA------BBCDCCCBDBDCDBDABCB---------CDCDBDCBBACACC----AB--B-AAABDBDCAAD--DDDACDCADCDBDCA--CDADDADABAADA--CDDA--------DAABBABDBAACB-BDCCBDDC-CDADDCCCCDABCB---CCBDDB------CBCCBDBBDAAAADBACDCCBCCDCBBC--CDCCCBDBD--AACBCDACDAAADBD------BBDBCBDADACCCDDBBDBDCCDD-CBDDCBBAC---AABBBBBBA----DDDDDDAB????????????????????????? ; END; BEGIN TREES; Title 'PPEITSMEGAML1000BSconsensusTreeGTR+G+IPartial Deletion Option'; LINK Taxa = Taxa; TRANSLATE 1 Cadophora_finlandica_AF486119, 2 Mycelium_radicis_atrovirens_AF486120, 3 Phialocephala_dimorphospora_AF486121, 4 Phialocephala_fusca_AF486122, 5 Sporendocladia_bactrospora_AF486123, 6 Phialocephala_fluminis_AF486124, 7 Phialocephala_compacta_AF486125, 8 Phialocephala_scopiformis_AF486126, 9 Kendrickiella_phycomyces_AF486127, 10 Phialocephala_xalapensis_AF486128, 11 Sporendocladia_foliicola_AF486129, 12 Sporendocladia_bactrospora_AF486130, 13 Phialocephala_humicola_AF486131, 14 Phialocephala_virens_AF486132, 15 Leptodontidium_orchidicola_AF486133, 16 Phialocephala_turiciensis_AY078128, 17 Phialocephala_turiciensis_AY078129, 18 Phialocephala_letzii_AY078130, 19 Phialocephala_cf._fortinii_AY078131, 20 Phialocephala_cf._fortinii_AY078132, 21 Phialocephala_europaea_AY078133, 22 Phialocephala_fortinii_AY078134, 23 Phialocephala_fortinii_AY078135, 24 Phialocephala_helvetica_AY078136, 25 Phialocephala_europaea_AY078137, 26 Phialocephala_fortinii_AY078138, 27 Phialocephala_fortinii_AY078139, 28 Phialocephala_fortinii_AY078140, 29 Phialocephala_fortinii_AY078141, 30 Phialocephala_helvetica_AY078142, 31 Phialocephala_fortinii_AY078143, 32 Phialocephala_fortinii_AY078144, 33 Acephala_applanata_AY078145, 34 Acephala_applanata_AY078146, 35 Acephala_applanata_AY078147, 36 Acephala_applanata_AY078148, 37 Acephala_applanata_AY078149, 38 Acephala_applanata_AY078150, 39 Acephala_applanata_AY078151, 40 Phialocephala_cf._fortinii_AY078152, 41 Sclerotinia_sclerotiorum_NW_001820801, 42 Phialocephala_fortinii_PPE5ITS, 43 Phialocephala_podophyllae_PPE7ITS; TREE PPE5&7_ITS_tree = ((((((((((((((((25:1.0,30:1.0):1.0,21:1.0):1.0,18:1.0):1.0,29:1.0):1.0,(24:1.0,(16:1.0,17:1.0):1.0):1.0):1.0,((28:1.0,27:1.0):1.0,((26:1.0,31:1.0):1.0,(32:1.0,22:1.0):1.0):1.0):1.0):1.0,((23:1.0,2:1.0):1.0,(19:1.0,(35:1.0,((36:1.0,37:1.0):1.0,((33:1.0,34:1.0):1.0,(38:1.0,39:1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0,(40:1.0,20:1.0):1.0):1.0,7:1.0):1.0,3:1.0):1.0,(43:1.0,8:1.0):1.0):1.0,15:1.0):1.0,1:1.0):1.0,(((42:1.0,9:1.0):1.0,6:1.0):1.0,((5:1.0,12:1.0):1.0,(4:1.0,(13:1.0,10:1.0):1.0):1.0):1.0):1.0):1.0,(14:1.0,11:1.0):1.0):1.0,41:1.0); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 478; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 478; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 478; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1408594602101; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7524775180941530539; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3410767723102256968; mqVersion 275; checksumv 0 3 3810998695 null getNumChars 478 numChars 478 getNumTaxa 43 numTaxa 43 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 1344880.0 sumSquares -2.0581954700241432E22 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 282; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 977 660; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7524775180941530539 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2752.1408539751338.5035220045139684447; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 695 593; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '(41:1.0,((11:1.0,14:1.0):1.0,(((6:1.0,(9:1.0,42:1.0):1.0):1.0,((5:1.0,12:1.0):1.0,(4:1.0,(10:1.0,13:1.0):1.0):1.0):1.0):1.0,(1:1.0,(15:1.0,((8:1.0,43:1.0):1.0,(3:1.0,(7:1.0,((20:1.0,40:1.0):1.0,(((2:1.0,23:1.0):1.0,(19:1.0,(35:1.0,((36:1.0,37:1.0):1.0,((33:1.0,34:1.0):1.0,(38:1.0,39:1.0):1.0):1.0):1.0):1.0):1.0):1.0,(((27:1.0,28:1.0):1.0,((22:1.0,32:1.0):1.0,(26:1.0,31:1.0):1.0):1.0):1.0,((24:1.0,(16:1.0,17:1.0):1.0):1.0,(29:1.0,(18:1.0,(21:1.0,(25:1.0,30:1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0):1.0);'; 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 on; 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 #3410767723102256968 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 310; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 695 593; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; 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 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;