#NEXUS [written Fri Feb 01 16:11:05 CET 2019 by Mesquite version 3.40 (build 877) at mdk-crou-006.cbs-niob.local/10.136.73.120] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=26; TAXLABELS Diaporthe_alleghaniensis_KC343249.1 Harknessia_cf._eucalyptorum_JQ706176.1 Harknessia_cf._eucalyptorum_JQ706178.1 Harknessia_fusiformis_JQ706179.1 Harknessia_fusiformis_AY720784.1 Harknessia_eucalyptorum_AY720809.1 Harknessia_eucalyptorum_AY720810.1 Harknessia_banksiigena_CPC_28232 Harknessia_banksiae_CPC_29002 Harknessia_banksiae_CPC_29443 'Harknessia banksiae-repens CPC 28874' 'Harknessia banksiae-repens CPC 29006' Harknessia_ravenstreetina_JQ706197.1 Harknessia_ravenstreetina_JQ706198.1 Harknessia_malayensis_CPC_28752 Harknessia_ellipsoidea_JQ706173.1 Harknessia_ellipsoidea_JQ706174.1 Harknessia_australiensis_JQ706170.1 Harknessia_australiensis_JQ706171.1 Harknessia_karwarrae_AY720811.1 Harknessia_platyphyllae_CPC_28862 Harknessia_pellitae_CPC_27606 Harknessia_communis_CPC_29028 Harknessia_communis_CPC_29038 Harknessia_communis_CPC_29468 Harknessia_communis_CPC_29470 ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "HarknessiaCAL.nexus"'; DIMENSIONS NCHAR=760; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Diaporthe_alleghaniensis_KC343249.1 ---------------CTTCTCCCTCTTTGTAAGTCATCTCCAGCCGGCAGACACGAGCTCCCCGCCCTCCTCTG---CTGGTGCGCATGATGCTAACGGACCGTTTTCGGCTTGTAGGATAAGGATGGCGATGGTTAGTGCGGCCGCCTCTTTACTCCCTCCCACCTACGCACGCG-TCATGTTCGATCCGCCGCGACAGCCTGCGCG-----TGCATAATTTCCAACCAAGCGAT-----------TATCACATCTATCACGAGTATCATGCTGAGATATGGCGTGTAGGGCAAATCACCACCAAGGAGCTCGGCACGGTCATGCGATCCCTGGGTCAGAACCCGTCCGAGTCTGAGTTGCAAGATATGATTAACGAGGTCGACGCCGACAACAATGGCACCATTGACTTCCCTGGTACGTCCAGATGCTCGCGCTCTGTGGGGG----GGGGGCTGGTGTCGCCCCTCTGCCGCA-GCCTCGTAACCACGTACTGACGCGTACCAACCAGAGTTCCTGACCATGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_cf._eucalyptorum_JQ706176.1 ---------ggaggccttctccctcttcgtgagtcacccacc---------------ttccaagccctcgtctgtgcctggggcgcgttcgctaacggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcctgataa-ccccatcccatc----gcaactg-tcgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgttggacgtacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtgtctagcgactccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttacaatgatggcca----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_cf._eucalyptorum_JQ706178.1 tgagttcaaggaggccttctccctcttcgtgagtcacccacc---------------ttccaagccctcgtctgtgcctggggcgcgttcgctaacggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcctgataa-ccccatcccatc----gcaactg-tcgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgttggacgtacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtgtctagcgactccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgacacgtccttcccgataagggtttccgaggcgagaaagtggttcaggagctgacgataagaccaggtctttgaccgcgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatctattggcgagaagctgaccgacgacgaggtggatgagatgat--- Harknessia_fusiformis_JQ706179.1 ----------gaggccttctcccttttcgtgagtcaaccacc---------------ttgcaagccctcgtctgtgccttgggcgcgttcgctaatagagcttcttcccaattacaggacaaggatggcgatggtgag--------cctctctcccccgccacgcttgcttgataa-ccccatcccatc----gcgactg-tcgcgcaaccgatgctgcagagccacatgcgcggtccctacaccatcgtcggacgtacg-aaaacaagaggctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctctgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgatttccctggtacgtcagagaccacgtggtttctaccgactccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagaattccttaccatgatggcca----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_fusiformis_AY720784.1 ---------ggaggccttctccctcttcgtgagtcaaccacc---------------ttgcaagccctcgtctgtgccttgggcgcgttcgctaatagagcttcttcccaattacaggacaaggatggcgatggtgag--------cctctctcccccgccacgcttgcttgataa-ccccatcccatc----gcgactg-tcgcgcaaccgatgctgcagagccacatgcgcggtccctacaccatcgtcggacgtacg-aaaacaagaggctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctctgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgatttccctggtacgtcagagaccacgtggtttctaccgactccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagaattccttaccatgatggcca----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_eucalyptorum_AY720809.1 ---------ggaggccttctccctcttcgtgagtcacccacc---------------tttcaagccctcgtctgtgccttgggcgcgttcgctaatggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-ccccatcctatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatagtcggacgtacg-aaaacatggagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgatttccctggtacgtcagagaccacgtggtgtctaccgactccgaggcccgtcgctgcctttcactgacacgattcgcgacta-------------------cagagttccttaccatgatggcca----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_eucalyptorum_AY720810.1 ---------ggaggccttctccctcttcgtgagtcacccacc---------------tttcaagccctcgtctgtgccttgggcgcgttcgctaatggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-ccccatcctatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatagtcggacgtacg-aaaacatggagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgatttccctggtacgtcagagaccacgtggtgtctaccgactccgaggcccgtcgctgcctttcactgacacgattcgcgacta-------------------cagagttccttaccatgatggcca----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_banksiigena_CPC_28232 tgagttcaaggaggccttctccctcttcgtgagtcacccacc---------------ttccaaacccttgtctgtgccttgggcgcgttcgctaacagagcttcttcccaacaccaggacaaggatggcgatggtgag--------cctct-tcccccgccacgcatgcttgataa-ccccatccaatc----gcaactg-ttgcgcaaccgatgctgcagggccacacgcgcgatccctacaccatcgtcggacgtacg-aaaacaagaagctaagata-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtgtctagcgactccgaggcccgtcgctgcctttcactgacccgactcgcgacta-------------------cagagttccttaccatgatggcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Harknessia_banksiae_CPC_29002 tgagttcaaggaggccttctccctcttcgtgagtcacccacc---------------ttccaaacccttgtctgtgccttgggcgcgttcgctaacagagcttcttcccaacaccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatacttgataacccccatccaatc----gcaactg-ttgcgcaaccgatgctgcagggccacacgcgcgacccttacaccatcgtcggacgtacgaaaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtgtctagcgaccccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_banksiae_CPC_29443 ------------ggccttctccctcttcgtgagtcacccacc---------------ttccaaacccttgtctgtgccttgggcgcgttcgctaacagagcttcttcccaacaccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatacttgataacccccatccaatc----gcaactg-ttgcgcaaccgatgctgcagggccacacgcgcgacccttacaccatcgtcggacgtacgaaaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtgtctagcgaccccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggctcgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgatacctccttcccgataagggtttccgtagcgagaaagtcgttcaggagctgacgaagagaccaggtctttgaccgtgac-------------------------------------------------------------------------------------------- 'Harknessia banksiae-repens CPC 28874' tgagttcaaggaggccttctccctcttcgtgagtcacccacc---------------ttccaaacccttggctgtgccatgggcgcgttcgctaacagagctccttcccaacaccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-ccccatccaatc----gcaactg-ttgcgcaaccgatgctgcagggccacacgcgcgatccctacaccatcgtcggacgtacg-aagacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacatggtgtctagcgactccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 'Harknessia banksiae-repens CPC 29006' tgagttcaaggaggccttctccctcttcgtgagtcacccacc---------------ttccaaacccttggctgtgccatgggcgcgttcgctaacagagctccttcccaacaccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-ccccatccaatc----gcaactg-ttgcgcaaccgatgctgcagggccacacgcgcgatccctacaccatcgtcggacgtacg-aagacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacatggtgtctagcgactccgaggcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Harknessia_ravenstreetina_JQ706197.1 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaccctccg-ctgtgccttgggcgcgttcgctaacggagcttcttcccaacatcaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-ccccatcccgtc----gcaactgcttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcggacgtacg-aaaacaagaagctaagatg-gccgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtctgagaccacgtggtgtttagcgactccgatgcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgaaacgtccttcctgatgagggtttctgtggcgagaaagtggttcaggagctgacgagaagatcaggtctttgaccgtgacaacaacggcttcatttcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtggatgagatgat--- Harknessia_ravenstreetina_JQ706198.1 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaccctccg-ctgtgccttgggcgcgttcgctaacggagcttcttcccaacatcaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-ccccatcccgtc----gcaactgcttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcggacgtacg-aaaacaagaagctaagatg-gccgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtctgagaccacgtggtgtttagcgactccgatgcccgtcgctgcctttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgaaacgtccttcctgatgagggtttctgtggcgagaaagtggttcaggagctgacgagaagatcaggtctttgaccgtgacaacaacggcttcatttcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtggatgagatgatcc- Harknessia_malayensis_CPC_28752 ----------gaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctccgctgtgccttgggcgcgttcgctaacggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctccccgccgccacgcatgcttgataa-ccccatcccgtc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcggacggacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtgtttggcgaccccgaggcctgtcgctgccgttcactgacacgactcgcgacta-------------------cagagttccttaccatgatggcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Harknessia_ellipsoidea_JQ706173.1 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctccgatgtgccttgggcgcgttcgctaacggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctctcccgccacgcatgcttgataa-ccccatcccgtc----gcaactg-ttgcgcaaccgatgctgcaaagccacacgcgcgattcctacaccatcgtcggacgtacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcag-gaccacgtggtgtttagcgactccgaggcctgtcgctgcctttcactaacacgactcgcgacta-------------------cagagttccttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgaaacgtccttcccgataaggatttccgcggcgagaaagttgcttaggagctgacgataataccaggtctttgaccgtgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtagatgagatgatccg Harknessia_ellipsoidea_JQ706174.1 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctccgatgtgccttgggcgcgttcgctaacggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctctcccgccacgcatgcttgataa-ccccatcccgtc----gcaactg-ttgcgcaaccgatgctgcaaagccacacgcgcgattcctacaccatcgtcggacgtacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcag-gaccacgtggtgtttagcgactccgaggcctgtcgctgcctttcactaacacgactcgcgacta-------------------cagagttccttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgaaacgtccttcccgataaggatttccgcggcgagaaagttgcttaggagctgacgataataccaggtctttgaccgtgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtagatgagatgatcc- Harknessia_australiensis_JQ706170.1 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctccgctgtgccttgggcgcgttcgctaatggagcttctttccaataccaggacaaggatggcgatggtgag--------cctcactcccccgccacgcatgcttgataa-ccccatgccatc----ccaactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcgaacgtacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgatgccgacaacaacggcaccatcgacttccctggtacgt-agagaccacgtggtgtctaccgactccgaggcccgtcgctgcctttcactgacacgacttgggacta-------------------cagagtttcttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgacacgtccttcccgataagggtttccgtgccgagaaagtggttcaggagctgacgataagaccaggtctttgaccgtgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtggatgagatgatcc- Harknessia_australiensis_JQ706171.1 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctccgctgtgccttgggcgcgttcgctaatggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctcactcccccgccacgcatgcttgataa-ccccatgccatc----ccaactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcgaacgtacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgt-agagaccacgtggtgtctaccgactccgaggcccgtcgctgcctttcactgacacgacttgcgacta-------------------cagagtttcttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagatccgcgaagccttcaaggtgcgacgcgtccttcccgataagggtttccgtgccgagaaagtggttcaggagctgacaataagaccaggtctttgaccgtgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtggatgagatgatc-- Harknessia_karwarrae_AY720811.1 ---------ggaggccttctccctcttcgtgagtcacccacc---------------ttccaagccctcgcctgtgccttgggcgctttcgctaacggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-cccaatcatatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcggacgtaca-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgactccgacaacaacggcaccatcgacttccccggtacgtcagagaccacgtggtgtctaccgactccgaggcccgtcgctgcctttcactgacacgaattggtacta-------------------cagagttccttaccatgatggcca----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_platyphyllae_CPC_28862 -------aaggaggccttctccctcttcgtgagtcacccacc---------------ttccaagccctcgcctgtgccttgggcgctttcgctaacggagcttcttcccaataccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-cccaatcatatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcggacgtaca-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctccgagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccccggtacgtcagagaccacgtggtgtctaccgactccgaggcccgtcgctgcctttcactgacacgacttgcgacta-------------------cagagtttcttaccatgatggcccgcaagatgaaggacaccgactctgaggaggagatccgcgaagccttcaaggtgcgacacgtccttcccgataagggtttccgtggcgagaaagtggtttaggagctgacgataagaccaggtctttgaccgtgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtggatgagatgatccg Harknessia_pellitae_CPC_27606 tgagttcaaggaggccttctccctcttcgtgagtcacccacc---------------ttccaaaccctcccctgtgccttgggcgcgttcgctgacggagcttcttcccaacaccaggacaaggatggcgatggtgag--------cctctctcccccgccacgcatgcttgataa-ccccatcctatc----gacactg-ttgcgcaaccgatgctgcagagccacacgcgcgatccctacaccatcgtcggacgtacg-aaaacaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctcggagtctgagctgcaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcaaagaccacgtggtgtctaccgactccgaggcccgtcgctgcctttcactgacacgacttgcgacta-------------------cagagtttcttaccatgatggcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Harknessia_communis_CPC_29028 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctcgtctgtgccttgggcgcgttcgctaacggagcttcttcccaactacaggacaaggatggcgatggtgag--------cctc--tcccccgccacgcatgcttgataa-ccccatcctatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgat-cctacaccatcgtcggacgtacg-aaagcaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctctgagtctgagctacaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtttctaccgactccgaggcccgtcgctgcctttcactgacacgacttgcgacta-------------------cagagtttcttaccatgat---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Harknessia_communis_CPC_29038 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctcgtctgtgccttgggcgcgttcgctaacggagcttcttcccaactacaggacaaggatggcgatggtgag--------cctc--tcccccgccacgcatgcttgataa-ccccatcctatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgat-cctacaccatcgtcggacgtacg-aaagcaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctctgagtctgagctacaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtttctaccgactccgaggcccgtcgctgcctttcactgacacgacttgcgacta-------------------cagagtttcttaccatgatggcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Harknessia_communis_CPC_29468 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctcgtctgtgccttgggcgcgttcgctaacggagcttcttcccaactacaggacaaggatggcgatggtgag--------cctc--tcccccgccacgcatgcttgataa-ccccatcctatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgat-cctacaccatcgtcggacgtacg-aaagcaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctctgagtctgagctacaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtttctaccgactccgaggcccgtcgctgcctttcactgacacgacttgcgacta-------------------cagagtttcttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagattcgcgaagccttcaaggtgcgacacgtcctttccgataagggtttccgtggcgagaaagtggttcaggtgctgacgataagaccaggtctttgaccgtgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtggatgagatgatcc- Harknessia_communis_CPC_29470 tgagttcaaggaggccttctccctcttcgtgagtcacgcacc---------------ttccaaaccctcgtctgtgccttgggcgcgttcgctaacggagcttcttcccaactacaggacaaggatggcgatggtgag--------cctc--tcccccgccacgcatgcttgataa-ccccatcctatc----gcaactg-ttgcgcaaccgatgctgcagagccacacgcgcgat-cctacaccatcgtcggacgtacg-aaagcaagaagctaagatg-gtcgtccaggtcaaatcaccaccaaggagctcggcaccgtcatgcgatcgctgggccagaacccctctgagtctgagctacaagacatgatcaacgaggtcgacgccgacaacaacggcaccatcgacttccctggtacgtcagagaccacgtggtttctaccgactccgaggcccgtcgctgcctttcactgacacgacttgcgacta-------------------cagagtttcttaccatgatggcccgcaagatgaaggacaccgactccgaggaggagattcgcgaagccttcaaggtgcgacacgtcctttccgataagggtttccgtggcgagaaagtggttcaggtgctgacgataagaccaggtctttgaccgtgacaacaacggcttcatctcggccgccgagctgcgccacgtcatgacatccattggcgagaagctgaccgacgacgaggtggatgagatgatccg ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 760; END; BEGIN PAUP; LOG start = yes append = yes; set autoclose = yes warnreset = no torder = right; OUTGROUP outgroups / only; exclude 1 - . / only; include combined / only; SET CRITERION = distance maxtrees = 1000 increase = no storebrlens = yes outroot = paraphyl; DSet distance = p; NJ breakties = random brlens = yes showtree = yes; Savetrees from = 1 to = 1 format = nexus brlens = yes maxdecimals = 6 file = HarknessiaCALuncorrectedp.tre; Bootstrap nreps = 1000 search = nj; Savetrees from = 1 to = 1 file = HarknessiaCALuncorrectedpbs.tre format = nexus brlens = yes savebootp = nodelabels maxdecimals = 0; DSet distance = k2p; NJ breakties = random brlens = yes showtree = yes; Savetrees from = 1 to = 1 format = nexus brlens = yes maxdecimals = 6 file = HarknessiaCALkimura2p.tre; Bootstrap nreps = 1000 search = nj; Savetrees from = 1 to = 1 format = nexus brlens = yes savebootp = nodelabels maxdecimals = 0 file = HarknessiaCALkimura2pbs.tre; DSet distance = hky85; NJ breakties = random brlens = yes showtree = yes; Savetrees from = 1 to = 1 format = nexus brlens = yes maxdecimals = 6 file = HarknessiaCALhky85.tre; Bootstrap nreps = 1000 search = nj; Savetrees from = 1 to = 1 format = nexus brlens = yes savebootp = nodelabels maxdecimals = 0 file = HarknessiaCALhky85bs.tre; SET CRITERION = parsimony maxtrees = 1000 increase = no storebrlens = yes outroot = paraphyl; Pset gapmode = newstate; HSEARCH ADDSEQ = random NREPS = 100 SWAP = TBR; roottrees ROOT = OUTGROUP OUTROOT = MONOPHYL; Savetrees format = nexus brlens = yes maxdecimals = 0 file = HarknessiaCALparsimony.trees; PSCORES 1 / TL = yes CI = yes RI = yes RC = yes HI = yes; Contree ALL / strict = yes treefile = HarknessiaCALparsimonycons.tre; Bootstrap nreps = 1000 search = heuristic; Savetrees from = 1 to = 1 format = nexus brlens = yes savebootp = nodelabels maxdecimals = 0 file = HarknessiaCALparsimonybootstrap.tre; Log stop = yes; END; BEGIN SETS; CHARSET combined = 16 - 43 58 - 139 147 - 190 194 - 491 510 - 527; TAXSET outgroups = 1; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 760; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 760; END; BEGIN TREES; Title 'Trees from "HarknessiaCALparsimony.trees"'; ID 0168a99ace2d1; LINK Taxa = Taxa; TRANSLATE [0] 1 Diaporthe_alleghaniensis_KC343249.1, [1] 2 Harknessia_cf._eucalyptorum_JQ706176.1, [2] 3 Harknessia_cf._eucalyptorum_JQ706178.1, [3] 4 Harknessia_fusiformis_JQ706179.1, [4] 5 Harknessia_fusiformis_AY720784.1, [5] 6 Harknessia_eucalyptorum_AY720809.1, [6] 7 Harknessia_eucalyptorum_AY720810.1, [7] 8 Harknessia_banksiigena_CPC_28232, [8] 9 Harknessia_banksiae_CPC_29002, [9] 10 Harknessia_banksiae_CPC_29443, [10] 11 'Harknessia banksiae-repens CPC 28874', [11] 12 'Harknessia banksiae-repens CPC 29006', [12] 13 Harknessia_ravenstreetina_JQ706197.1, [13] 14 Harknessia_ravenstreetina_JQ706198.1, [14] 15 Harknessia_malayensis_CPC_28752, [15] 16 Harknessia_ellipsoidea_JQ706173.1, [16] 17 Harknessia_ellipsoidea_JQ706174.1, [17] 18 Harknessia_australiensis_JQ706170.1, [18] 19 Harknessia_australiensis_JQ706171.1, [19] 20 Harknessia_karwarrae_AY720811.1, [20] 21 Harknessia_platyphyllae_CPC_28862, [21] 22 Harknessia_pellitae_CPC_27606, [22] 23 Harknessia_communis_CPC_29028, [23] 24 Harknessia_communis_CPC_29038, [24] 25 Harknessia_communis_CPC_29468, [25] 26 Harknessia_communis_CPC_29470; TREE First_of_six_equally_most_parsimonious_trees_obtained_from_the_Harknessia_calmodulin_alignment = (((2:1,3:0.0):2,(((4:1,5:0.0):13,(6:0.0,7:0.0):6):4,((((13:0.0,14:0.0):10,((16:0.0,17:0.0):6,15:6):2):2,(((20:5,21:0.0):6,((23:0.0,24:0.0,25:0.0,26:0.0):11,22:5):2):3,(18:3,19:0.0):7):3):2,((9:0.0,10:0.0):6,(11:0.0,12:0.0):5,8:3):5):1):2):59,1:105):0.0; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1549033865252; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8135107521988980836; tell It; setDefaultOrder 25 0 1 2 3 4 5 15 11 12 13 14 6 7 20 9 10 23 24 8 22 21 16 17 18 19; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4360983807564885741; mqVersion 340; checksumv 0 3 3251176432 null getNumChars 760 numChars 760 getNumTaxa 26 numTaxa 26 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 265423.0 sumSquares -4.166658317649145E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 609; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1450 848; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8135107521988980836 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8135107521988980836; getWindow; tell It; useTargetValue off; setTargetValue ; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 841 776; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; setActive; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8135107521988980836 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 0168a99ace2d1; toggleUseWeights off; endTell; setAssignedID 995.1549033724294.220485549222754407; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 841 776; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 off; toggleEven off; setFixedTaxonDistance 0; endTell; setEdgeWidth 6; orientRight; 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 off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '(1:105,((2:1,3:0.0):2,(((4:1,5:0.0):13,(6:0.0,7:0.0):6):4,((8:3,(9:0.0,10:0.0):6,(11:0.0,12:0.0):5):5,(((13:0.0,14:0.0):10,(15:6,(16:0.0,17:0.0):6):2):2,((18:3,19:0.0):7,((20:5,21:0.0):6,(22:5,(23:0.0,24:0.0,25:0.0,26:0.0):11):2):3):3):2):1):2):59):0.0;'; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; 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; toggleShow consensusFrequency; toggleShow bootstrapFrequency; toggleShow posteriorProbability; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4360983807564885741 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 841 776; 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; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.AlterData.AlterData; tell It; toggleBySubmenus off; 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 16 6 1 1; 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;