#NEXUS [written Sun Jul 07 11:12:55 CEST 2013 by Mesquite version 2.75 (build 564) at Jan-PC/192.168.2.103] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=26; TAXLABELS Pythium_arrhenomanes_P54 Pythium_sp._Hybrid_1_Isolate Pythium_sp._Hybrid_7_Isolates Pythium_phragmiticola_P56 Pythium_phragmiticola_P90 Pythium_phragmiticola_P113 Pythium_phragmiticola_P114 Pythium_phragmiticola_P119 Pythium_phragmiticola_P120 Pythium_phragmiticola_P125 Pythium_phragmiticola_P126 Pythium_phragmitis_P13 Pythium_phragmitis_P40 Pythium_phragmitis_P42 Pythium_phragmitis_P52 Pythium_phragmitis_P55 Pythium_phragmitis_P58 Pythium_phragmitis_P59 Pythium_phragmitis_P61 Pythium_phragmitis_P62 Pythium_phragmitis_P63 Pythium_phragmitis_P65 Pythium_phragmitis_P69 Pythium_phragmitis_P71 Pythium_phragmitis_P73 Pythium_graminicola_AF196593 ; END; BEGIN CHARACTERS; TITLE Pythium_phragmiticola_cox_II_sequences; DIMENSIONS NCHAR=563; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Pythium_arrhenomanes_P54 ATGGAAGGTATTATTAACTTTCATCATGATTTAATGTTTTTCCTAATTAT Pythium_sp._Hybrid_1_Isolate ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_sp._Hybrid_7_Isolates ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P56 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P90 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P113 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P114 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P119 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P120 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P125 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmiticola_P126 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P13 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P40 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P42 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P52 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P55 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P58 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P59 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P61 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P62 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P63 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P65 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P69 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P71 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_phragmitis_P73 ATGGAAGGTATTATAAACTTTCACCATGATTTAATGTTTTTCTTAATTAT Pythium_graminicola_AF196593 ATGGAAGGTATTATTAACTTTCACCATGATTTAGTGTTTTTCTTAATTAT Pythium_arrhenomanes_P54 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_sp._Hybrid_1_Isolate TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_sp._Hybrid_7_Isolates TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P56 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P90 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P113 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P114 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P119 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P120 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P125 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmiticola_P126 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P13 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P40 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P42 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P52 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P55 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P58 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P59 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P61 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P62 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P63 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P65 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P69 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P71 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_phragmitis_P73 TGTAACTGTTTTTGTTTGTTGGATGTTATTTAGAGTTATTACATTATTTG Pythium_graminicola_AF196593 TGTAACAGTTTTTGTTTGTTGGATGTTATTTAGAGTAATAACATTATTTG Pythium_arrhenomanes_P54 ATGAAAAAAAAAATCCTATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_sp._Hybrid_1_Isolate ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_sp._Hybrid_7_Isolates ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P56 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P90 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P113 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P114 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P119 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P120 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P125 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmiticola_P126 ATGAAAAAAAAAATCCTATTCCTGCTACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P13 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P40 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P42 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P52 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P55 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P58 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P59 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P61 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P62 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P63 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P65 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P69 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P71 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_phragmitis_P73 ATGAAAAAAAAAATCCAATTCCTGCGACATTTGTACATGGAGCTACTATA Pythium_graminicola_AF196593 ATGAAAAAAAAAACCCTATTCCTGCTACATTTGTACATGGTGCTACTATA Pythium_arrhenomanes_P54 GAAATTATTTGGACAACAATTCCTGCTTTAATTTTATTAACTGTAGCAGT Pythium_sp._Hybrid_1_Isolate GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_sp._Hybrid_7_Isolates GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P56 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P90 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P113 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P114 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P119 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P120 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P125 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmiticola_P126 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P13 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P40 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P42 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P52 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P55 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P58 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P59 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P61 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P62 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P63 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P65 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P69 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P71 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_phragmitis_P73 GAAATTATTTGGACAACAATACCTGCTTTAATTTTATTAACCGTAGCTGT Pythium_graminicola_AF196593 GAAATTATTTGGACAACTATTCCTGCTTTAATTTTATTAACAGTAGCTGT Pythium_arrhenomanes_P54 ACCATCATTTGCTTTATTATATTCTATGGATGAAATCATAGATCCTATTA Pythium_sp._Hybrid_1_Isolate ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_sp._Hybrid_7_Isolates ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P56 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P90 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P113 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P114 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P119 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P120 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P125 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmiticola_P126 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P13 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P40 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P42 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P52 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P55 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P58 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P59 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P61 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P62 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P63 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P65 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P69 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P71 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_phragmitis_P73 ACCATCATTTGCTTTATTATATTCTATGGATGAAATTATAGATCCTATTA Pythium_graminicola_AF196593 ACCTTCTTTTGCTTTATTATATTCTATGGATGAAATTATTGATCCTATTA Pythium_arrhenomanes_P54 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCC Pythium_sp._Hybrid_1_Isolate TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_sp._Hybrid_7_Isolates TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P56 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P90 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P113 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P114 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P119 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P120 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P125 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmiticola_P126 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P13 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P40 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P42 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P52 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P55 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P58 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P59 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P61 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P62 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P63 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P65 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P69 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P71 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_phragmitis_P73 TTACTTTAAAAGTAATTGGTAGTCAATGGTATTGGAGTTATGAATATTCT Pythium_graminicola_AF196593 TTACTGTTAAAGTAATTGGTAGTCAATGGTATTGGAGCTATGAATATTCT Pythium_arrhenomanes_P54 GATAATTTGGAATTTGCTGACGAACCTTTAATTTTTGATAGTTATATGGT Pythium_sp._Hybrid_1_Isolate GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_sp._Hybrid_7_Isolates GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P56 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P90 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P113 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P114 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P119 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P120 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P125 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmiticola_P126 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P13 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P40 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P42 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P52 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P55 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P58 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P59 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P61 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P62 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P63 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P65 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P69 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P71 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_phragmitis_P73 GATAATTTAGAATTTGCTGATGAACCTTTAATTTTTGATAGTTATATGGT Pythium_graminicola_AF196593 GATAATTTAGAATTTGCAGATGAACCTTTAATCTTTGATAGTTATATGGT Pythium_arrhenomanes_P54 ACAAGAAAATGATTTAGAAATAGGACAATTGAGACTTTTAGAAGTAGATA Pythium_sp._Hybrid_1_Isolate GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_sp._Hybrid_7_Isolates GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P56 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P90 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P113 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P114 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P119 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P120 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P125 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmiticola_P126 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P13 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P40 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P42 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P52 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P55 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P58 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P59 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P61 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P62 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P63 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P65 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P69 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P71 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_phragmitis_P73 GCAAGAAAATGATTTAGAAATAGGACAATTCAGACTTTTAGAAGTTGATA Pythium_graminicola_AF196593 ACAAGAAAATGACTTAGAAATCGGACAATTTAGACTTTTAGAAGTTGACA Pythium_arrhenomanes_P54 ATCGTGTTGTTGTACCTACAAATAGTCATATAAGAGTGTTAATAACAGCT Pythium_sp._Hybrid_1_Isolate ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_sp._Hybrid_7_Isolates ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P56 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P90 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P113 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P114 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P119 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P120 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P125 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmiticola_P126 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGGGTATTAATAACAGCT Pythium_phragmitis_P13 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P40 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P42 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P52 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P55 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P58 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P59 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P61 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P62 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P63 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P65 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P69 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P71 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_phragmitis_P73 ACCGTGTTGTTGTACCTACAAATAGTCATATTAGAGTATTAATAACAGCT Pythium_graminicola_AF196593 ACCGCGTTGTTGTGCCTACAAACAGTCATATTAGAGTATTAATAACAGCT Pythium_arrhenomanes_P54 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_sp._Hybrid_1_Isolate TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_sp._Hybrid_7_Isolates TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P56 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P90 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P113 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P114 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P119 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P120 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P125 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmiticola_P126 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P13 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P40 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P42 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P52 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P55 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P58 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P59 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P61 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P62 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P63 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P65 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P69 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P71 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_phragmitis_P73 TCAGATGTATTACATTCTTGGGCTATACCATCTTTAGGTGTTAAATTAGA Pythium_graminicola_AF196593 TCTGATGTTTTACACTCTTGGGCTATTCCTTCTTTAGGTGTTAAATTAGA Pythium_arrhenomanes_P54 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_sp._Hybrid_1_Isolate TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_sp._Hybrid_7_Isolates TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P56 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P90 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P113 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P114 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P119 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P120 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P125 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmiticola_P126 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P13 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P40 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P42 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P52 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P55 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P58 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P59 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P61 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P62 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P63 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P65 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P69 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P71 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_phragmitis_P73 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_graminicola_AF196593 TGCTTGTCCAGGTCGTTTAAATCAAACTTCTATGTATATTAAAAGAGAAG Pythium_arrhenomanes_P54 GTGTTTTTTATGG Pythium_sp._Hybrid_1_Isolate GTGTTTTTTATGG Pythium_sp._Hybrid_7_Isolates GTGTTTTTTATGG Pythium_phragmiticola_P56 GTGTTTTTTATGG Pythium_phragmiticola_P90 GTGTTTTTTATGG Pythium_phragmiticola_P113 GTGTTTTTTATGG Pythium_phragmiticola_P114 GTGTTTTTTATGG Pythium_phragmiticola_P119 GTGTTTTTTATGG Pythium_phragmiticola_P120 GTGTTTTTTATGG Pythium_phragmiticola_P125 GTGTTTTTTATGG Pythium_phragmiticola_P126 GTGTTTTTTATGG Pythium_phragmitis_P13 GTGTTTTTTATGG Pythium_phragmitis_P40 GTGTTTTTTATGG Pythium_phragmitis_P42 GTGTTTTTTATGG Pythium_phragmitis_P52 GTGTTTTTTATGG Pythium_phragmitis_P55 GTGTTTTTTATGG Pythium_phragmitis_P58 GTGTTTTTTATGG Pythium_phragmitis_P59 GTGTTTTTTATGG Pythium_phragmitis_P61 GTGTTTTTTATGG Pythium_phragmitis_P62 GTGTTTTTTATGG Pythium_phragmitis_P63 GTGTTTTTTATGG Pythium_phragmitis_P65 GTGTTTTTTATGG Pythium_phragmitis_P69 GTGTTTTTTATGG Pythium_phragmitis_P71 GTGTTTTTTATGG Pythium_phragmitis_P73 GTGTTTTTTATGG Pythium_graminicola_AF196593 GTGTATTCTATGG ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 563; END; BEGIN TREES; Title Pythium_phragmiticola_cox_II_ML_tree; LINK Taxa = Taxa; TRANSLATE 1 Pythium_arrhenomanes_P54, 2 Pythium_sp._Hybrid_1_Isolate, 3 Pythium_sp._Hybrid_7_Isolates, 4 Pythium_phragmiticola_P56, 5 Pythium_phragmiticola_P90, 6 Pythium_phragmiticola_P113, 7 Pythium_phragmiticola_P114, 8 Pythium_phragmiticola_P119, 9 Pythium_phragmiticola_P120, 10 Pythium_phragmiticola_P125, 11 Pythium_phragmiticola_P126, 12 Pythium_phragmitis_P13, 13 Pythium_phragmitis_P40, 14 Pythium_phragmitis_P42, 15 Pythium_phragmitis_P52, 16 Pythium_phragmitis_P55, 17 Pythium_phragmitis_P58, 18 Pythium_phragmitis_P59, 19 Pythium_phragmitis_P61, 20 Pythium_phragmitis_P62, 21 Pythium_phragmitis_P63, 22 Pythium_phragmitis_P65, 23 Pythium_phragmitis_P69, 24 Pythium_phragmitis_P71, 25 Pythium_phragmitis_P73, 26 Pythium_graminicola_AF196593; TREE tree_1 = (26:0.040381,(1:0.023491,((5:0.0,(4:0.0,(6:0.0,(3:0.0,(7:0.0,(8:0.0,(9:0.0,(11:0.0,10:0.0)inode9:0.0)inode8:0.0)inode7:0.0)inode6:0.0)inode5:0.0)inode4:0.0)inode3:0.0)inode867:0.00338,((25:0.0,24:0.0)inode10:0.0,(23:0.0,(2:0.0,(22:0.0,(18:0.0,(((15:0.0,14:0.0)inode17:0.0,(13:0.0,12:0.0)inode18:0.0)inode16:0.0,(16:0.0,(17:0.0,(19:0.0,(21:0.0,20:0.0)inode22:0.0)inode21:0.0)inode20:0.0)inode19:0.0)inode15:0.0)inode14:0.0)inode13:0.0)inode12:0.0)inode11:0.0)inode857:0.001962)inode676:0.005944)inode2:0.01689)root; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 563; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 563; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1373188375739; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4872416638186566794; tell It; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 485161128335226367; mqVersion 275; checksumv 0 3 3059091825 null getNumChars 563 numChars 563 getNumTaxa 26 numTaxa 26 short true bits 15 states 15 sumSquaresStatesOnly 425902.0 sumSquares 425902.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 249; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1366 694; setLocation -4 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #4872416638186566794 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 877.1373187560385.3181442297573628305; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1117 627; setLocation -4 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; 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 #485161128335226367 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1117 627; setLocation -4 -4; 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; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; 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;