#NEXUS [written Wed Mar 20 12:25:25 EDT 2013 by Mesquite version 2.74 (build 550) at cesar-herreras-MacBook-Pro.local/10.109.194.193] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=23; TAXLABELS Cosmospora_coccinea_AR2741 Cosmospora_stegonsporii_AR4385 Corallomycetella_repens_AR4547 Pseudocosmospora_eutypellae_AR4562 Microcera_larvarum_AR4580 Pseudonectria_pachysandricola_AR4592 Pseudocosmospora_joca_AR4779 Cosmospora_viridescens__CBS102433 Dialonectria_episphaeria_CH1001 Dialonectria_sp_CH1014 Pseudocosmospora_eutypae_CH1101 Dialonectria_sp_CH1106 Dialonectria_sp_GJS091197 Cosmospora_viliuscula_GJS09411 Cosmospora_viliuscula_GJS10247 Cosmospora_viliuscula_GJS83197 Cosmospora_viliuscula_GJS86315 Pseudocosmospora_rogersonii_GJS9056 Microcera_coccophila_GJS9850 Cosmospora_flavoviridis_IMI338173 Microcera_coccophila_MF241482 Cosmospora_obscura_MF241484 Pseudocosmospora_vilior_PC1246 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=580; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Cosmospora_coccinea_AR2741 gacgcgtt---------cctcat--gcgagcccctgatt-ctaccccgccgaaac-attcca-cca-c-cgtcgggccatatc---gcagcttcag-gcaca--gacgccatgtgatgcttgggaactggagggaacaaagattgctgaccatgtgg-ttttttgcgacataggttcacatccagaccggtcagtgcgtaagt-aactctgc-----at------gctgtcgtgt--tgcggatcgac---caactcaccatgtttcaatagggtaaccaaattggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaatggtgtctacaacggcacctccgagctccagctcgagcgcatgagcgtctacttcaacgaggtacg---t--ggaaatcacctcacttttggctg------------gtttcggctatt--gacacgtc--ttaggcctccggcaacaagtatgtccctcgcgccgttctcgtcgatctcgagcccggtaccatggacgccgtccgtgccggtcccttcggccagctcttccgtcccgacaacttc Cosmospora_stegonsporii_AR4385 gacgcgtc---------cctgatcagagagcccctgattcctaccccgccgaagc-aatcca-cca-cccgtcgggccatattgcagcaacttcag-acgca--gacacgatgtgatattt----------gggaat-gttatggctaacaatgtga-ttttctgtatcataggttcacctccagaccggtcagtgcgtaagt-aactcgcc-----at------ttcaacgtgt--tgcggaccgac---gaactcacaatgttttgatagggtaaccaaatcggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaatggtgtctacaacggtacctctgagctccagctcgagcgcatgagcgtctacttcaacgaggtacg---c--aacaatcaccccattcacgcttt------------ctttcggctact--gactcgtc--ttaggcttccggcaacaagtatgtccctcgcgctgtcctcgtcgatcttgagcctggtaccatggacgccgtccgtgccggtcctttcggccagctcttccgccccgacaacttc Corallomycetella_repens_AR4547 gacgcgtc---------cctgatc-aggagcccctgagc-ctaccccgccgaggc-atcccataacataggtcaggctgtatc---acagcttcaagacacaagaacacgacgcgatatgt----------ggaaac-gtcatggctaactgtgcggtttttttgcgacataggttcacctccagaccggccagtgcgtaagt-agctcaac-----gc------tcgatattgt--tgcgacccgacacgaagctcaccacgttgcgatagggtaaccaaatcggtgccgctttctggcagaccatctctggcgagcatggtcttgacagcaatggtgtctacaacggcacctctgagcttcagctggagcgcatgagcgtctacttcaacgaggtacgggcc--gaaaatcaccccatgcttccgcatccgctg-----tgaccagcacct--gacacgtcgtctaggcctctggcaacaagtatgttcctcgcgccgttctcgtcgatctcgagcccggcaccatggatgccgtccgtgccggtcctttcggccagctcttccgccccgacaacttc Pseudocosmospora_eutypellae_AR4562 gacgcgtt---------tctgat--cagagcccctgatt-ctaccccgccgaagc-attcca-cca-cacaacgggtgatatc---gcagcttcaggacatt--ggcaaaatatgatgcat----------ttggacaacgattgctaaccatatgatttttccgggatacaggttcaccttcagaccggtcagtgcgtaagt-aactcgct-----g-------ttcgacgtgt--cgtccgtccgc---aaactcacattgttgtgatagggtaaccaaattggtgctgctttctggcagactatctctggcgagcacggtctcgacagcaacggcgtctacaatggcacctctgagctccagctcgagcgcatgagcgtctacttcaacgaggtacg---c--gaaatttaccttattcgcgctt-------------ccctcggttact--gacacgtt-cataggcctctggcaacaagtatgtccctcgcgccgttctcgtcgatcttgagcccggtaccatggacgccgtccgtgccggtcctttcggtcagctcttccgtcccgacaacttc Microcera_larvarum_AR4580 aacgcgtt---------cttgatc-gtgagcccctgatt-ctaccccgccgaacc-attcga-cct-catatcgagccacatc---ggagctttc--acaaa--tgcacgaagggatactt----------gagaata--gatggctaaccgtgttg-ttttctctga-ataggttcaccttcagaccggtcagtgcgtaagt-tactcacc--------ttgctgtctgtacac--tacgagtgcgg---gaactcacgatatttccatagggtaaccaagttggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaatggtgtctacaacggcacctctgagcttcagctcgagcgcatgagcgtttacttcaacgaggtatg---c--aaaaatatttcaccccacaaagtg-----------tgttcggcagct--gacacgtc--ctaggcctctggcaacaagtatgtccctcgcgccgtccttgtcgatcttgagcccggtaccatggacgccgtccgtgccggtcccttcggccagctcttccgtcccgacaacttc Pseudonectria_pachysandricola_AR4592 gacgcgtcttgtaccagcttgggggaggagcccctgatc-ctaccccgccgaaacaaatcca-cca-cccgatgcacgacttgac-gcgattccgg-gtaca--gactggatattttgatg----------gaacgagttggctaacgatttcttcc-tttttgctattataggttcacctccagaccggtcagtgcgtaagt-gctatcctctccgatgttggcttcactatgc--gggggatttgc--------taacatcgtccgacagggtaaccaaatcggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaacggtgtctacaatggcacctctgagctccagctcgagcgcatgagcgtctacttcaacgaggtacg---t--agaacgctacagccgagttcgcaagcaccaaaagacgtgaagctgacaggctacaac--ataggcctccggcaacaagtatgttcctcgcgctgtcctcgtcgatctcgagcccggtaccatggacgccgtccgtgccggtcccttcggccagcttttccgccccgacaacttc Pseudocosmospora_joca_AR4779 gacgcgtc---------cctgatc-agaggcccctgatt-ctaccccgccgaagc-attcca-cca-cacgtcgggccagatc---ccacctgcag-acaca--agcacgatatcatactc----------aggaacaatgattgctaac-atttgg-ttttttgcgacttaggttcacctccagaccggtcagtgcgtaagt-aactcacc-----t-------ttcaacgtgt--tgtcgatccgc---aaactcacgatgctgtgttagggtaaccaaattggtgccgctttctggcagaccatttctggcgagcacggcctcgacagcaacggtgtttacaatggcacttctgagcttcagcttgagcgcatgagcgtctacttcaacgaggtacg---ttgagaaaagaacttgttcgcgctt-------------ctctgggtcact--gacacgct--ctaggcctctggaaacaagtatgtccctcgcgccgtcctcgtcgatcttgagcccggtaccatggacgccgtccgtgccggtcctttcggtcagcttttccgtcccgacaacttc Cosmospora_viridescens__CBS102433 gacgcgtt---------cctgat--cagagcccctgatt-ctaccccgccgacac-attcca-cca-cccgtcgtgccatatc---gcagcttcag-acaca--gacgcgatgtgatactt----------gggaacaaagattgctaaccatgtgg-ttttctgcgacataggttcacctccagaccggtcagtgcgtaagt-aactcatc-----at------gctgttgtgt--tgccgatcgac---gaactcacgatgttctaatagggtaaccaaatcggtgctgctttctggcagaccatctctggcgagcatggcctcgacagcaatggtgtctacaacggcacctctgagctccagctcgagcgcatgagcgtctacttcaacgaggtacg---c--ggaaatcgcctcatttgtggtt-------------gtttcggctatt--gacacttc--ttaggcctctggcaacaagtatgtccctcgcgccgttctcgtcgatctcgagcccggtaccatggacgccgtccgtgccggtcccttcggtcagctcttccgtcccgacaacttc Dialonectria_episphaeria_CH1001 gacgcgtc---------cgtgatc-aggagcccctgatt-ctaccccgccgaagc-attcca-ctt-cacatagggccatatc---acagcttcgg-acacg--aacaaactgtggtgttctg--------gggaacaatgattgctaaccatgtgg-ttttccgcgacataggttcacctccagaccggtcagtgcgtaagt-aactcgtc-----a-------gttgccgtgt--cgcgaagcgtc---gaactcacaatgttatgatagggtaaccaaattggtgctgctttctggcagaccatttctggcgagcacggccttgacagcaatggtgtctacaatggtacctctgagctccagctcgagcgcatgagcgtctacttcaacgaggtaag--------gagccaccgcctcgacgcgttttctctccctatttttcagctgct--gacacgtg--ctaggcctctggcaacaaatatgtccctcgcgccgtcctcgtcgatcttgagcctggtaccatggacgccgtccgagccggtcctttcggtcagctcttccgtcccgacaacttc Dialonectria_sp_CH1014 gacgcgtc---------cgtgatc-aggagcccctaatt-ctaccccgccgaagc-attcca-ctt-cacggagggccatatc---acagctttgg-acaca--aacaagatgtgatgttctg--------gggaacaatgattgctaacgatgtgg-ttttccgcgacataggttcacctccagaccggtcagtgcgtaagt-aactcatc-----a-------gttgtcgtgtgccgcgaaacgtc---gaactcaccatgttatgatagggtaaccagatcggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaa-ggtgtctacaatggtacctctgagcttcaactcgagcgtatgagcgtctacttcaacgaggtaaa--------aa-ccaccgcctacacgcgtttttcctcccta-atttcagctact--gacacgtg--gtaggcctctggcaacaaatatgtccctcgcgccgtcctcgtcgatcttgagcctggtaccatggacgctgtccgagccggtcctttcggtcagctcttccgtcccgacaacttc Pseudocosmospora_eutypae_CH1101 ------------------------------cccctgatt-ctaccccgccgaagc-attcca-cca-cacgtcgggcc--atc---gcagcttctg-acaca--gacacgatataatgctt----------gggaacaatgattgctaaccatgtggtttttctgcgacataggttcacctccagaccggccagtgcgtaagt-aactcacc-----at-tcgaattcgacgtgt--tgccgatcaac---aaactcaccatattgtgatagggtaaccaaattggtgctgctttctggcagactatttctggcgagcatggcctcgacagcaatggtgtctacaatggcacttctgagctccagctcgagcgtatgagcgtctacttcaacgaggtacg---t--agagttcttttttctcacgatttttttagtgctc-cgttcggctact--gacgtgcc--ataggcctctggcaacaagtatgtccctcgcgccgtcctcgtcgatcttgagcccggtaccatggatgctgtccgtgccggtcctttcggtcagctctt---------------- Dialonectria_sp_CH1106 gacgcgtc---------cgcgatc-aggagcccctgatttctaccccgccgaagc-attcca-cttccccgttgggccatatc---gcagctttgg-acacg-ggatacgacgtgatgctcttgagaacaaacgaaccaagattgctaaccatgtgg-ttttctgcgacataggttcacctccagaccggtcagtgcgtaagtcaattcgcc-----a-------gtcgacgtgc--cgcggattatc---aaactcaccatgttgtgatagggtaaccaaatcggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaatggtgtctataacggtacctctgagctccagctcgagcgtatgagcgtctacttcaatgaggtatg---a--agaagccaccgcctacgcgttcccctcctcttta-cttgcggctact--gacgctct--ttaggcttctggaaacaagtatgtccctcgcgccgtcctcgtcgatcttgagcctggtaccatggatgccgtccgcgctggtcctttcggtcagctcttccgtcccgacaacttc Dialonectria_sp_GJS091197 gacgcgtc---------cgtgatc-aggagcccctgatt-ctaccccgccgaagc-attcca-ctt-cacgtcgggccaaatc---gcagcttcgg-actca--gacacgatgtgatgctctg--------gggaacaatgattgctgaccatgtgg-ttttccacgacataggttcacctccagaccggtcagtgcgtaagt-aactcgtt-----g-------gttgtcgtgc--cgcgaaatgtc---gaactcaccatgttatgatagggtaaccaaatcggtgctgctttctggcagactatctctggcgagcatggcctcgatagcaatggcgtctacaatggtacctctgagcttcagctcgagcgtatgagcgtctacttcaacgaggtatg--------gagccaccgtttacacgcgtttgccctccttc-ttttcagctact--gacacctt--gtaggcctccggcaacaaatatgtccctcgcgccgtcctcgtcgatcttgagcctggtaccatggacgccgtccgcgccggtcctttcggtcagctcttccgtcccgacaacttc Cosmospora_viliuscula_GJS09411 gacgcgtt---------cctgat--tagagcccctgact-ttaccccgccgaaac-attcca-cct-cttgtcgggctatatc---gcagcttcag-aaaca--gacgcgatgcgatgctt----------aggaacaatgattgctaaccatgtga-ttttctgcgacataggttcaccttcagaccggccagtgcgtaagt-aactcacc-----gt------ctcgtcatat--cgcggatcggc---aagctcacgaaatcttgacagggtaaccaaatcggtgctgctttctggcagaccatctctggcgagcatggcctcgacagcaatggtgtctacaacggcagctctgagctccagcttgagcgtatgagcgtctacttcaacgaggtacg---g--gggaatccgcttacttgcagtc-------------gacacagctatt--gacacgtc--ttaggcttctggcaacaagtatgtccctcgcgccgttctcgtcgatctcgagcctggtaccatggacgccgtccgtgccggtccctttggccagctcttccgtcccgacaacttc Cosmospora_viliuscula_GJS10247 gacgcgtt---------cctgat--cagagcccctgatt-ctaccccgccgaaac-attcca-cct-ccgttgggcccatatc---gcagcttcgg-acaca-ggacgcgatacgatgctg----------gggaacaacaattgctaaccatgtgt-ttttctgcgacataggttcacctccagaccggtcagtgcgtaagt-aactcatt-----gt------gtcgacgtgt--tggggacgaca---aaactcacggtgtcttgacagggtaaccaaatcggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaatggtgtctacaacggaacctctgagctccagctggagcgcatgagcgtctacttcaacgaggttcg---t--gggcacagctttactattgtg--------------ggtgcggctatt--gacacgcc--ttaggcttccggcaacaagtatgtccctcgcgccgttctcgtcgatctcgagcctggtaccatggatgccgtccgtgctggtccctttggccagctcttccgtcctgacaacttc Cosmospora_viliuscula_GJS83197 gacgcgtt---------cctgatc-cagagcccctgatt-ttaccccgccgaaac-attccaccct-cacgtcgggccatatc---gcagcttcagaacatc--gacgcgatgtgatgcttg---------gggaacaacgattgctaaccatgtgg-ttttctgcgacataggttcacctccagaccggtcagtgcgtaagt-aactcgcc-----at------gctgccgtgc--tgcggatcgac---aaactcacgatttcttgatagggtaaccaaattggtgctgctttctggcagaccatttctggcgagcatggcctcgacagcaatggtgtctacaacggcacttctgagctccagctcgagcgcatgagcgtctacttcaacgaggtacg---c--gaaaatgccttcacttgtgctt-------------gggtcggttatt--gacacgtc--ttaggcttctggtaacaagtatgtccctcgcgccgtcctcgtcgatctcgagcccggtaccatggatgccgttcgcgctggtcccttcggtcagctcttccgtcccgacaacttt Cosmospora_viliuscula_GJS86315 gacgcgtt---------cctgat---agcgcccctgatt--taccccgccgaaac-attcca-cct-tgggtcgggccatatg---gcagcttcag-accca--gacgcgatatgatgctt----------gagaacaacgattgctgactctttga-ttttctgcgatataggttcacctccagaccggtcagtgcgtaagt-aactcact-----at------ctcgtcaggt--cgcggatcggc---aagctcacgatgtcttgatagggtaaccaaatcggtgctgctttctggcagaccatctctggcgagcatggcctcgacagcaatggcgtctacaacggcagctctgagctccagcttgagcgtatgagcgtttacttcaacgaggtacg---g--ggaaataccctcacttctgggc-------------gatttggccatt--gacacgtc--ttaggcatctggaaacaagtatgtccctcgcgccgtcctcgtcgatctcgagcctggtaccatggacgctgtccgtgccggccccttcggccagctcttccgtcccgacaacttc Pseudocosmospora_rogersonii_GJS9056 gacgcgtt---------tctgat--cagagcccctgatt-ctaccccgccgaagc-attcca-cca-cacaacgggtgatatc---gcagcttcacgatatt--ggcacaatatgatccgt----------ttggacaacgattgctaaccatataatttttccgtgatataggttcaccttcagaccggtcagtgcgtaagt-agctcgcc-----g-------ttcgacgtgt--cgtccgtccat---aaactcacattgttgtgatagggtaaccaaattggtgctgctttctggcagaccatctctggcgagcacggtctcgacagcaatggtgtctacaatggcacctctgagctccagctcgagcgtatgagcgtctacttcaacgaggtacg---c--gaaatgtaccctattcgcgctt-------------ccctcggttact--gacacgtt-tataggcctctggcaacaagtatgtccctcgcgccgttctcgtcgatcttgagcccggtacaatggacgccgtccgtgccggtcctttcggtcagctcttccgtcccgacaacttc Microcera_coccophila_GJS9850 aacgcgtt---------cctgatc-gcgagcccctgatt-ttaccccaccgaagt-attcga-cct-caggtcgtgccacact---gaaagcttct-acaca--tgcacgaagcgatactt----------gggaacg--tatggctaacgactttg--tttctccga-acaggttcacctccagaccggtcagtgcgtaagttaactcacc-----atgttcctgccaacacgt--tacgagcgggg---aaactcacgatgcttcgatagggtaaccaaattggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaatggtgtctacaatggcacttccgagctccagctcgagcggatgagcgtttacttcaacgaggtacg---t--ggatatagcctcccttttgtcggtt----------gttttggccact--gacacgtt--gcaggcatctggcaacaagtatgtccctcgcgctgtcctcgtcgatcttgagcccggtaccatggatgccgtccgtgccggtcctttcggtcagctcttccgtcctgacaacttc Cosmospora_flavoviridis_IMI338173 gacgcgtc---------cctggc--cagagcccctgatt-ctaccccgccgaggc-cttcca-cca-cacgtggagccatatcgcagcagcttcgg-acaca--gacacgatatgatattc----------gagaac-atgatggctaactacgtgg-ttttccgtgatataggttcacctccagaccggtcagtgcgtaagt-aactcact-----at------ttcgacatgt--tgccggccgac---gaactcacgatgtt-tgatagggcaaccaaattggtgctgctttctggcagaccatctctggcgagcatggcctcgacagcaatggtgtctataacggcacctccgagctccagctcgagcgcatgagcgtctacttcaacgaggtatg---c--ggaaatcaccccattcgcgtttt------------atttcggctact--gacgcttc--tcaggcctctggcaacaagtatgtccctcgcgccgtcctcgtggatcttgagcccggtaccatggacgccgtccgtgccggtccttttggccagctcttccgccccgacaacttc Microcera_coccophila_MF241482 aacgcgtt---------cttgatc-gtgagcccctgatt-ttaccccgccgaaac-attcga-cct-catatcgagccacatg---ggagcttcc--acaaa--tgcacgaagtgatactt----------gggaat---gatggctaaccgtgttg-ttttctctga-ataggttcacctccagaccggtcagtgcgtaagt-tactcacc--------ttgctgtctgtacgc--tacgagtgcgg---gaactcacgatatttcgatagggtaaccaagttggtgctgctttctggcagaccatctctggcgagcacggcctcgacagcaatggtgtctacaacggcacctctgagcttcagctcgagcgcatgagcgtctacttcaacgaggtatg---c--aaaaaaattccatctcgcaaagtg-----------tgttcggcagct--gacacgtc--ctaggcctctggcaacaagtatgtccctcgcgccgtcctcgtcgatcttgagcccggtaccatggatgccgtccgtgccggtcctttcggccagctcttccgtcccgacaacttc Cosmospora_obscura_MF241484 gacgcgtc---------cctgagc-cagagcccctgatt-ctaccccgccgaggc-cttcca-cca-cacgtcgagccatatcgcagcagcttcgg-ataca--gacacgacgtgatatttga--------gagaac-atgatggctaactacgtgg--tttctgtgatataggttcacctccagaccggtcagtgcgtaagt-aactcact-----at------ttcgacgtgt--tgccggccgac---ggactgaccatgtt-tgatagggcaaccaaatcggtgctgctttctggcagaccatctctggcgagcatggcctcgacagcaatggtgtctacaacggcacctccgagcttcagctcgagcgcatgagcgtctacttcaacgaggtacg---t--agaaatcacctcattcgcgcttt------------atttcggctact--gacacttc--tcaggcctccggcaacaagtatgtccctcgcgccgtcctcgtcgatcttgagcccggtaccatggacgccgtccgtgccggtcctttcggccagctcttccgccccgacaacttc Pseudocosmospora_vilior_PC1246 gacgcgtc---------cttgct--cagagcccctgatt-ctaccccgccgaagc-attcca-ccaccatgtcgggccatatt---gcagcttcag-acaca--gtcacgacataattgtt----------gggaacgacgattgctaaccatgtg--ccttcttcgatacaggttcacctccagaccggtcagtgcgtaagt-acttcacc-----at------tcgaacgtgtggcgccgatccac---gaactcacgttcttgtattagggtaaccaaattggtgctgctttctggcaaaccatttctggcgagcacggccttgacagcaatggtgtctacaatggcacctctgagctccagctcgagcgcatgagcgtctacttcaacgaggtgcg---t--acaatctctctt-ctatcgcgc-------------tcctcggcaact--gacacgtt--gtaggcctctggcaacaagtatgtccctcgcgccgtcctcgtcgatttggagcccggtaccatggacgccgtccgtgccggtcccttcggtcagctcttccgtcccgacaacttc ; END; begin mrbayes; outgroup Corallomycetella_repens_AR4547; lset applyto = ( 1 ) nst = 6 rates = gamma; unlink shape = ( all ) pinvar = ( all ) statefreq = ( all ) revmat = ( all ); prset ratepr = variable; mcmcp ngen = 5000000 relburnin = yes burninfrac = 0.25 printfreq = 1000 samplefreq = 100 nchains = 4 savebrlens = yes; mcmc; sumt burnin = 12500 contype = halfcompat; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 580; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 580; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 580; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1363796725549; linkFile '../../Trees/overview/tub_overview.nex.con.txt'; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7625419330625288527; tell It; setSelected 3; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6001233845354138699; mqVersion 274; checksumv 0 2 604443557 null getNumChars 580 numChars 580 getNumTaxa 23 numTaxa 23 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 248527.0 sumSquares -4.4341361067179335E21 NumFiles 2 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7625419330625288527 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlockInt 0; toggleUseWeights off; endTell; setAssignedID 865.1363796701716.3933648278383066216; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; 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 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 '(3:0.1138815,((2:0.023922,6:0.549778)0.96:0.043907,(20:0.037368,22:0.020357)1.00:0.044592,((7:0.105354,11:0.066272,(23:0.120641,(4:0.021232,18:0.02586)1.00:0.094981)0.57:0.013892)0.98:0.027006,((19:0.136022,(5:0.034545,21:0.008586)1.00:0.087502)1.00:0.112134,(12:0.089533,(13:0.04434,(9:0.041941,10:0.026126)1.00:0.023797)1.00:0.034317)1.00:0.071097,((1:0.052869,8:0.02563)0.87:0.013101,(16:0.056481,(15:0.12253,(14:0.062402,17:0.070247)1.00:0.035435)0.56:0.015971)0.98:0.018833)0.98:0.038352)0.55:0.008484)0.88:0.018104):0.1138815);'; 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; 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 #6001233845354138699 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 22; 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;