正选择分析

作者: 多啦A梦的时光机_648d | 来源:发表于2020-11-12 11:21 被阅读0次

一:准备核酸序列和树文件

## 核酸序列(长度不一样比对去gap)
      5 3372
FJ973621Lhes
GCTCAAGCACAGGCAGAAGCAGCAGCCCGTGCTCAGGCACAAGCAGAAGCCAGAGCTAAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCAGAAGCCAGAGCTAAAGCTGAAGCCACAGCTCGTGCCAAAGCACAAGCGGAAGCAGCAGCACGTGCTCAAGCACAAGCAGAAGCCAGAGCTATAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCAGAAGCTAGAGCTAAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCCATAGCGAGAGCTGAAGCTGCTGCGCGTGCTCAGGCTGAAGCAGAGGCGCGTGCATATGCTGAAGCTTTAGCAAGAGTTCAAGCTGAAGCTGCTGCTAGAGCTCAAGCACAAACTCAATCCAGAACTCAAGCTGAAACACATTCTCAAGCACATAGTGCTTCTCATGCATCTTCTCAAGCAACCTCTGAGACTCACGTTGAAAGTACTGCCCATACTGCTACAGAAACGCATGAACATACGTCTTCTAACTCTCAAGCTGCCAGTCACACCCAAGCAGCTTCTCACAGTCAAGCAAAAGCTCAAAGTGAAGCACATACGTATTCTCAAGCTCAATCAGCCGCACATACTATTGCCGCAGCTCAAGCACAAGCTGAAACCAGAGCCAGAGCTGAAGCTGTTGCTAGAGCGCAAGCACAAGCGGAGGCCAGAGTGAGAGCAGAAGCAGCAGCCCGTGCTCAAGCACAAGCCGAAGCAGCAGCCCGTGCTCAAGCACAAGCCGAAGCAGCAGCCCGTGCTCAAGCACAAGCCGAAGCAGCAGCCCGTGCTCAAGCACAAGCCGAAGCAGCAGCCCGTGCTCAAGCACAAGCCGAAGCAGCAGCCCGTGCTCAAGCACAAGCCGAAGCAGCAGCCCGTGCTCAATCACAATCTGAAGCAGCCGCACGTGCTCAAGCTCAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGTTGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCTGCAGCCCGTGCTCAGGCACAAGCCGAAGCCAGAGCTAAAGCTGAAGCAGCAGTCCGTGCTCAAGCTCAAGTTGAAGCAGCAGCCCGTGCTCAAGCACAAGTGGAAGCTGCAGCCCGTGCTCAAGCACAGGCAGAAGCAGCAGCCCGTGCTCAGGCACAAGCAGAAGCCAGAGCTAAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCAGAAGCCAGAGCTAAAGCTGAAGCCACAGCTCGTGCCAAAGCACAAGCGGAAGCAGCAGCACGTGCTCAAGCACAAGCAGAAGCCAGAGCTATAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCAGAAGCTAGAGCTAAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCCATAGCGAGAGCTGAAGCTGCTGCGCGTGCTCAGGCTGAAGCAGAGGCGCGTGCATATGCTGAAGCTTTAGCAAGAGTTCAAGCTGAAGCTGCTACTAGAGCTCAAGCACAAACTCAATCCAGAACTCAAGCTGTAACACATTCTCATGCCCATAGTGCTTCTCATGCATCTTCTCAAGCATCCTCTGAGACTTACGCAGAAAGTACTGCTCATACTGCTACAGAAACGCATGAACATACGTCTTCTCACTCTCAAACTGCCAGTCACAGCCAAGCAGCTTCTCACAGTAAAGCAAAAGCTCATACTGAAGCAGATACGTATTCTCAAGCTCAATCAGCCGCACATACTATTGCCGCTGCTCAAGCACAAGCGGAAACTAGAGCCAGAGCTGAAGCTGTTGCTAGAGCGCAAGCACAAGCAGAAGCCAGAGTTAGAGCAGAAGCAGCAGCTCGTGCTCAAGCACAAGCTGAAGCAGCAGCCCGTGCTCATGCACAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCCAGAGCTAAAGCTGAAGCAGCAGCCCGCGCTCAAGCACAGGCAGAAGCCAGAGCTAAAGCTGAAGCAGCAGCCCGTGCTCAAGCACAAGCAGAAGCCAGAGCGAGAGCTGAAGCAGTAGCCCGTGCTCAAGCACAAGCGGAAGCAGCAGCTCGTGCTCAAGCACAAGCGGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCAGCAGCCCGTGCTCAAGCACAAGCGGAAGCAGCAGCCCGTGCTCAAGCACAAGCAGAAGCCAGAGCGAGAGCAGAAACTGCTGCGCGAGCTCAGGCTGAAGCAGAGGCGCGTGCATATGCTGAAGCTTTAGCAAGAGTTCAAGCTGAAGCTGCTGCTAGAGCTCAAGCACAATCTCAATCCAGAATTCAAGCTGAAACACAGTCTCATGCACATAGTGCTTCTCATGCATCTTCTCAAGCATTCTCTGAGACTCACGCGGAAAGTGCTGCCCATACTGCTACAGAAACGCATGAACAGACGTCTTCTCACTCACAAGCTGCCAGTCGAAGTCAAGCAGCTTCTCACAGTCAAGCAGAAGCTCATACTGAAGCACATACGTATTCTCAAGCTCAGTCAGCCGCACATACTATTGCCGCAGCTCAAGCACAAGCGGAAACAAGAGCCAGAGCTGAAGCTGCTGCTCGAGCGCAAGCACATGCTCAAGCTGAAGCTGTTGCACGAGCTCGAGCAGAAGCAGCTGCCAGAGCCAAAGCACAGGCGGAAGCACGTGCTGATGCAGAAGCTGCCGCAAAAGCTCAAGCTGAAGCTGCAGCATTAGCTCATGCACAAGCTGTTGCTCGTGCTCAAGCAGAAGCTGCTGCCAAAGCTAAAATAGAAGAAGAAGCACGTGCTCAAGCTGAAGCGGCAATCAGGTCTCAAGTAGAAGCTGCAGTTAGAGCTCAAGCTGAAGCACATTCTCAAGCAAAATCCGAAGCAAGCACTCAAACGCAAACTGCGGCATATTCGAGCAGTGAAAGTGCTTCCTCCTCTGAAGCTGAATCTTCTTCATACGCACAATCCTTCCAGTTTTCACTCACATACACGCTGCATTAACGTCTTCAGCTCATCAGTTGGTCTCTGCAGCAGCTAAACGCAGAATTGCTTCGCTATCGCAAGCTATGTCTTCTGTTATCTCCGGAGGTGCGTTAACTACGCAGCTCTTTCCAGCTCTTTATCTGGCTTAGCGAGTGAAATCCAAAATGAATCCAACTTATCAAAAACAGAAGTTCTCGTCGAAGCTTTACTGGAAACATTGTCAGCTCTTTTGGA
KY398016Aarg
GCTAGAGCTGTAGCCCAGTCCCTCGGATTGTCACAAGGGTCAGTTCAAAATATAATGAGCCAACAATTGAGCAGCATAGGCTCTGGAGCTTCCACATCATCCCTCTCCCAGGCGATAGCAAATGCCGTATCTTCCGCAGTTCAAGGATCACAGGCAGCAGCTCCAGGACAGGAACAATCTATTGCACAAAGAGTAAATTCAGCCATTTCCTCCGCTTTCGCACAATTGATTTCCCAGAAAACCGCACCGGCTCCGGCCCCGAGACCCAGACCAGCTCCNTTGCCTGCTCCAGCTCCAAGGCCCAGACCAGCACCTGCTCCACGACCAGCACCAGTTTATGCACCAGCGCCAGTTGCTTCGCAATTTCAGGCGTCTGCTTCCAGTCAATCTTCGGCTCAAGAGAATTCCTTCACTCAGTCATCAGTTGCTCAGCAATCAGCAGTTGCCCAACAATCCTCAGTTTCTCAACAATCCTCAGCTGCTCAACAGTCATCAGTTGCTCAATCGCAACAAACATCTTACTCTGCAGCAACAAATGCCGGTTCGAGTGTCTCGCAGTCTCAAGCTATTGTCTCAAGTGCCCCTGTGTACTTCAACTCGCAAACTTTGACAAACAACTTGGCTTCCTCTCTGCAATCACTGAATGCTCTTAATTACGTATCGAATGGTCAATTGAGTTCCTCGGATGTCGCTTCCACTGTTGCTAGAGCTGTAGCCCAGTCCCTCGGATTGTCACAAGGGTCAGTTCAAAATATAATGAGCCAACAATTGAGCAGCATAGGCTCTGGAGCTTCCACATCATCCCTCTCCCAGGCGATAGCAAATGCCGTATCTTCCGCAGTTCAAGGATCACAGGCAGCAGCTCCAGGACAGGAACAATCTATTGCACAAAGAGTAAATTCAGCCATTTCCTCCGCTTTCGCACAATTGATTTCCCAGAGAACCGCACCGGCTCCGGCCCCGAGACCCAGACCAGCTCCATTGCCTGCTCCAGCTCCAAGGCCCAGACCAGCACCTGCTCCACGACCAGCACCANTTTATGCACCAGCGCCAGTTGCTTCGCAATTTCAGGCGTCTGCTTCCAGTCAATCTTCGGCTCAACAGAATTCCTTCACTCAGTCATCAGTTGCTCAGCAATCAGCAGTTGCCCAACAATCCTCAGTTTCTCAACAATCCTCAGCTGCTCAACAGTCATCAGTTGCTCAATCGCAACAAACATCTTACTCTGCAGCAACAAATGCCGGTTCGAGTGTCTCGCAGTCTCAAGCTATTGTCTCAAGTGCCCCTGTGTACTTCAACTCGCAAANTTTGACAAACAACTTGGCTTCCTCTCTGCAATCACTGAATGCTCTTAATTACGTATCGAATGGTCAATTGAGTTCCTCGGATGTCGCTTCCACTGTTGCTAGAGCTGTAGCCCAGTCCCTCGGATTGTCACAAGGGTCAGTTCAAAATATAATGAGCCAACAATTGAGCAGCATAGGCTCTGGAGCTTCCACATCATCCCTCTCCCAGGCGATAGCAAATGCCGTATCTTCCGCAGTTCAAGGATCACAGGCAGCAGCTCCAGGACAGGAACAATCTATTGCACAAAGAGTAAATTCAGCCATTTCCTCCGCTTTCGCACAATTGATTTCCCAGAGAACCGCACCGGCTCCGGCCCCGAGACCCAGACCAGCTCCATTGCCTGCTCCAGCTCCAAGGCCCAGACCAGCACCTGCTCCACGACCAGCACCAGTTTATGCACCAGCGCCAGTTGCTTCGCAATTTCAGGCGTCTGCTTCCAGTCAATCTTCGGCTCAAGAGAATTCCTTCACTCAGTCATCAGTTGCTCAGCAATCAGCAGTTGCCCAACAATCCTCAGTTTCTCAACAATCCTCAGCTGCTCAACAGTCATCAGTTGCTCAATCACAACAAACATCTTACTCTGCAGCAACAAATGCCGGTTCGAGTGTCTCGCAGTCTCAAGCTATTGTCTCAAGTGCCCCTGTGTACTTCAACTCGCAAACTTTGACAAACAACTTGGCTTCCTCTCTGCAATCACTGAATGCTCTTAATTACGTATCGAATGGTCAATTGAGTTCCTCGGATGTCGCTTCCACTGTTGCTAGAGCTGTAGCCCAGTCCCTCGGATTGTCACAAGGGTCAGTTCAAAATATAATGAGCCAACAATTGAGCAGCATAGGCTCTGGAGCTTCCACATCATCCCTCTCCCAGGCGATAGCAAATGCCGTATCTTCCGCAGTTCAAGGATCACAGGCAGCAGCTCCAGGACAGGAACAATCTATTGCACAAAGAGTAAATTCAGCCATTTCCTCCGCTTTCGCACAATTGATTTCCCAGAGAACCGCACCGGCTCCGGCCCCGAGACCCAGACCAGCTCCATTGCCTGCTCCAGCTCCAAGGCCCAGACCAGCACCTGCTCCACGACCAGCACCAGTTTATGCACCAGCGCCAGTTGCTTCGCAATTTCAGGCGTCTGCTTCCAGTCAATCTTCGGCTCAAGAGAATTCCTTCACTCAGTCATCAGTTGCTCAGCAATCAGCAGTTGCCCAACAATCCTCAGTTTCTCAACAATCCTCAGCTGCTCAACAGTCATCAGTTGCTCAATCGCAACAAACATCTTACTCTGCAGCAACAAATGCCGGTTCGAGTGTCTCGCAGTCTCAAGCTATTGTCTCAAGTGCCCCTGTGTACTTCAACTCGCAAACTTTGACAAACAACTTGGCTTCCTCTCTGCAATCACTGAATGCTCTTAATTACGTATCGAATGGTCAATTGAGTTCCTCGGATGTCGCTTCCACTGTTGCTAGAGCTGTAGCCCAGTCCCTCGGATTGTCACAAGGGTCAGTTCAAAATATAATGAGCCAACAATTGAGCAGCATAGGCTCTGGAGCTTCCACATCATCCCTCTCCCAGGCGATAGCAAATGCCGTATCTTCCGCAGTTCAAGGATCACAGGCAGCAGCTCCAGGACAGGAACAATCTATTGCACAAAGAGTAAATTCAGCCATTTCCTCCGCTTTCGCACAATTGATTTCCCAGAGAACCGCACCGGCTCCGGCCCCGAGACCCAGACCAGCTCCATTGCCTGCTCCAGCTCCAAGGCCCAGACCAGCACCTGCTCCACGACCAGCACCAGTTTATGCACCAGCGCCAGTTGCTTCGCAATTTCAGGCGTCTGCTTCCAGTCAATCTTCGGCTCAAGAGAATTCCTTCACTCAGTCCCAACAATCCTCAGTTTCTCAACCTCAACAGTCATCAGTTGCTCAATCGCAACAAACATCTTACTCTGCAGCAACAAATGCCGGTTCGAGTGTCTCGCAGTCTCAAGCTATTGTCTCAAGTGCCCCTGTGTACTTCAACTCGCAA
LC570228Osyb
GCTAATTCATACAGGGCCAATTACAATACTTTCCAGCAGTCTGTAGCATCTGCTTTTGCAACTTCGCGTTCGTTTAGTTCTTTGAACACGCAAGTAGTCAGAACGGAAGATGTCAGAAACGTATTAAGTAGCGTTCTGCAGAGAAGAGGCATTTCATCTTCCGCTATCCAAAGTGCAATTAGTAGAATTAATCTAAGCGCTGGATCGTCTGTCGGAGCTTATTCTCAATCTATTTCTTCGGCATTAACGGCAGCAATGCAACAGAGCAGTATGCTATCTTCTGGACAGGAGCAAAGCATGGCAAGCTCGATTGCAACCGAAGTGATGCAAAGTTTGCTTCACATATCAACGCAGAAATCTCGTCCAGCAGCACCACGTCCCGCTCCCCTTCCCAGACCAGCCCCGAGACCTATGCCCCGTCCAATGCCTGCACCGATGCCAGTACAACAAACCCAAGTTATGCAATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTACTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACTGCATCACAGGTCTCTTCCACAAGTCAAGTATCTTCAGGATCTAGCTCTTTGAGTGCTAATTCATACAGGGCCAATTACAATACTTTCCAGCAGTCTGTAGCATCTGCTTTTGCAACTTCGCGTTCGTTTAGTTCTTTGAACACGCAAGTAGTCAGAACGGAAGATGTCAGAAACGTATTAAGTAGCGTTCTGCAGAGAAGAGGCATTTCATCTTCCGCTATCCAAAGTGCAATTAGTAGAATTAATCTAAGCGCTGGATCGTCTGTCGGAGCTTATTCTCAATCTATTTCTTCGGCATTAACGGCAGCAATGCAACAGAGCAGTATGCTATCTTCTGGACAGGAGCAAAACATGGGAGGCATGATTGCAACCGAAGTGATGCAAAGTTTGCTTCAAATATCAACGCAGAAATCTCGTCCAGCAGCACCACGTCCCGCTCCCCTTCCCAGACCAGCCCCGAGACCTATGCCCCGTCCAATGCCTGCACCGATGCCAGTACAACAAACCCAAGTTATGCAATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACTGCATCACAGATCTCTTCCACAAGTCAAGTATCTTCAGGATCTAGCTCTTTGAGTGCTAATTCATACAGGGCCAATTACAATACTTTCCAGCAGTCTGTAGCATCTGCTTTTGCAACTTCGCGTTCGTTTAGTTCTTTGAACACGCAAGTAGTCAGAACGGAAGATGTCAGAAACGTATTAAGTAGCGTTCTGCAGAGAAGAGGCATTTCATCTTCCGCTATCCAAAGTGCAATTAGTAGAATTAATCTAAGCGCTGGATCGTCTGTCGGAGCTTATTCTCAATCTATTTCTTCGGCATTAACGGCAGCAATGCAACAGAGCAGTATGCTATCTTCTGGACAGGAGCAAAGCATGGCAAGCTCGATTGCAACCGAAGTGATGCAAAGTTTGCTTCACATATCAACGCAGAAATCTCGTCCAGCAGCACCACGTCCCGCTCCCCTTCCCAGACCAGCCCCGAGACCTATGCCCCGTCCAATGCCTGCACCGATGCCAGTACAACAAACCCAAGTTATGCAATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTACTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACTGCATCACAGGTCTCTTCCACAAGTCAAGTATCTTCAGGATCTAGCTCTTTGAGTGCTAATTCATACAGGGCCAATTACAATACTTTCCAGCAGTCTGTAGCATCTGCTTTTGCAACTTCGCGTTCGTTTAGTTCTTTGAACACGCAAGTAGTCAGAACGGAAGATGTCAGAAACGTATTAAGTAGCGTTCTGCAGAGAAGAGGCATTTCATCTTCCGCTATCCAAAGTGCAATTAGTAGAATTAATCTAAGCGCTGGATCGTCTGTCGGAGCTTATTCTCAATCTATTTCTTCGGCATTAACGGCAGCAATGCAACAGAGCAGTATGCTATCTTCTGGACAGGAGCAAAACATGGGAGGCATGATTGCAACCGAAGTGATGCAAAGTTTGCTTCAAATATCAACGCAGAAATCTCGTCCAGCAGCACCACGTCCCGCTCCCCTTCCCAGACCAGCCCCGAGACCTATGCCCCGTCCAATGCCTGCACCGATGCCAGTACAACAAACCCAAGTTATGCAATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACTGCATCACAGGTCTCTTCCACAAGTCAAGTATCTTCAGGATCTAGCTCTTTGAGTGCTAATTCATACAGGGCCAATTACAATACTTTCCAGCAGTCTGTAGCATCTGCTTTTGCAACTTCGCGTTCGTTTAGTTCTTTGAACACGCAAGTAGTCAGAACGGAAGATGTCAGAAACGTATTAAGTAGCGTTCTGCAGAGAAGAGGCATTTCATCTTCCGCTATCCAAAGTGCAATTAGTAGAATTAATCTAAGCGCTGGATCGTCTGTCGGAGCTTATTCTCAATCTATTTCTTCGGCATTAACGGCAGCAATGCAACAGAGCAGTATGCTATCTTCTGGACAGGAGCAAAGCATGGCAAGCTCGATTGCAACCGAAGTGATGCAAAGTTTGCTTCACATATCAACGCAGAAATCTCGTCCAGCAGCACCACGTCCCGCTCCCCTTCCCAGACCAGCCCCGAGACCTATGCCCCGTCCAATGCCTGCACCGATGCCAGTACAACAAACCCAAGTTATGCAATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTACTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACCGCATCACAGGCTGCTGCAGCATCATACCAAAGTGCCGCAACTTCTGCATCGACTGCATCACAGGTCTCTTCCACAAGTCAAGTATCTTCAGGATCTAGCTCTTTGAGTGCTAATTCATACAGGGCCAATTACAATACTCAGTCTGTAGCATCTGCTTTTGCAACTTCGCGTTCCAGAACGGAAGATGTCAGAAACGTT
MH376748Aven
GCGAGTGCGGTAGCACCGTCACTTGGAGTGTCCCAAGCGTCGGTTCAAAATAGTATAAGCCAACAGTTGAGAAGCGTAGGGCCCGGATCTTCCACGTCCTCTGTCGCTCAAGCAATAGCAAATGGAGTGGCTAACGCAGTTGGAGCATCAGGAACAGGAGTTGCAGGACAAGAACAATCTATTTCACAATCCATATATACTTCAGTTTCCACTGCTCTATCTCAACTGGCAGCACCGGCTCCAGCACCTGCACCTAGACCAGCTCCTCGACCACTACCAGCCCCAATTCAAGCCCCAAGACCAGCACCCGCACCACAACCTGCACCGGTTTACGCACCAGCCCCAGTCGTTTCACAAGTTCAGGCAACTTCTTCCTCTCAAGCCTCGGCTCAACAGAGTGCCTTCGCACAGTCCCAACAATCTTCAGTTGTTCAATCTCAACAAAGCTCAAACGCTTATTCTGCAGCTTCATCTGTAGGCTCAAGTTTTTCGCAGTCTCAGGGGACTGTCCCAAGCGCTCCTGTTTATTTTAACACGCAAACTTTAAGTAGCAGCCTGTCTTCTTCTCTGCAATCACTCAGTGCACTCAATTCGATAGCGAGTGGTCAACTGAGCTCCTCGAATGCCGCTTCTATTATAGCGAGTGCAGTGGCACGGTCACTTGGAGTGTCCCAAGCGTCGGTTCAAAATAGTATAAGCCAACAGTTGAGAAGCGTAGGGCCCGGATCTTCCACGTCCTCTGTCGCTCAAGCAATAGCAAATGGAGTGGCTAACGCAGTTGGAGCATCAGGAACTGGAGTTGCAGGACAAGAACAATCTATTTCACAATCCATATATACTTCAATTTCCACTGCTCTTTCTCAACTGGCAGCACCGGCTCCAGCACCTGCACCGAGACTTGCTCCTAGACCACTACCAGCCCCAATTCAAGCCCCAAGACCAGCACCCGCACCACAACCTGCACCGGTTTACGCACCAGCCCCAGTCGTTTCACAAGTTCAGGCAACTTCTTCCTCTCAAGCTTCGGCTCAACAGAGTGCCTTCGCACAGTCCCAGCAATCTTCAGTTGCACAATCTCAACAAAGCTCAAACGTTGATTCTGCAGCTTCATCTGTAGGCTCAAGTTTTTCGCAGTCTCAGGGGACTGTCCCAAGCGCTCCTGTTTATTTTAACACGCAAACTTTAAGTAGCAGCCTGTCTTCTTCTCTGCAATCACTCAGTGCACTCAATTCGATAGCGAGTGGTCAACTGAGCTCATCGTATGCCGATTCTATTTTAGCGAGTGCAGTGGCTCGGTCTCTTGGAGTTTCCCAAGCGTCGGTTCTAAATAGTATAAGCCAACAGTTGAGAAGCGTAGGGCCCGGATCTTCCACGTCCTCTGTCGCTCAAGCAATAGCAAATGGAGTGGCTAACGCAGTTGGAGCATCAGGAACAGGAGTTGCAGGACAAGAACAATCTATTTCACAATCCATATATACTTCAGTTTCCACTGCTCTTTCTCAACTGGCAGCACCGGCTCCAGCACCTGCACCGAGACTTGCTCCTAGACCACTACCAGCCCCAATTCAAGCCCCAAGACCAGCACCCGCACCACAACCTGCACCGGTTTACGCACCAGCCCCAGTCGTTTCACAAGTTCAGGCAACTTCTTCCTCTCAAGCCTCGGCTCAACAGAGTGCCTTCGCACAGTCCCAACAATCTTCAGTTGTTCAATCTCAACAAAGTTCAAACGCTTATTCTGCAGCATCAACTGCCGGTTCAAGTGTGTCGCAATCTCAGGCGATTGTCTCAAGCGCTCCTGATTATTTTAACACGCAAACTTTAAGTAGCAGCCTGTCTTCTTCTCAGCAATCACTCAGTGCACTCAATTCGATAGCGAGTGGTCAACTGAGCTCCTCGAATGCCGCTTCTATTTTAGCGAGTGCAGTGGCACGGTCACTTGTAGTGTCCCACGCGTCGGTTCAAAATAGTATAAGCCAACAGTTGAGAAGCGTAGGGCCCGGATCTTCCACGTCCTCTGTCGCTCAAGCAATAGCAAATGGAGTGGCTAACGCAGTTGGAGCATCAGGAACTGGAGTTGCAGGACAAGAACAATCTATTTCACAATCCATATATACTTCAATTTCCACTGCTCTTTCTCAACTGGCAGCACCGGCTCCAGCACCTGCACCGAGACTTGCTCCTAGACCACTACCAGCCCCAATTCAAGCCCCAAGACCAGCACCCGCACCACAACCTGCACCGGTTTACGCACCAGCCCCAGTCGTTTCACAAGTTCAGGCAACTTCTTCCTCTCAAGCCTCGGCTCAACAGAGTGCCTTCGCACAGTCCCAACAATCTTCAGTTGTTCAATCTCAACAAAGTTCAAACGCTTATTCTGCAGCATCAACTGCCGGTTCAAGTGTGTCGCAATCTCAGGCGATTGTCTCAAGCGCTCCTGATTATTTTAACACGCAAACTTTAAGTAGCAGCCTGTCTTCTTCTCAGCAATCACTCAGTGCACTCAATTCGATAGCGAGTGGTCAACTGAGCTCCTCGAATGCCGCTTCTATTTTAGCGAGTGCAGTGGCACGGTCACTTGGAGTGTCCCAAGCGTCGGTTCAAAATAGTATAAGCCAACAGTTGAGAAGCGTAGGGCCCGGATCTTCCACGTCCTCTGTCGCTCAAGCAATAGCAAATGGAGTGGCTAACGCAGTTGGAGCATCAGGAACTGGAGTTGCAGGACAAGAACAATCTATTTCACAATCCATATATACTTCAATTTCCACTGCTCTTTCTCAACTGGCAGCACCGGCTCCAGCACCTGCACCGAGACTTGCTCCTAGACCACTACCAGCCCCAATTCAAGCCCCAAGACCAGCACCCGCACCACAACCTGCACCGGTTTACGCACCAGCCCCAGTCGTTTCACAAGTTCAGGCAACTTCTTCCTCTCAAGCCTCGGCTCAACAGAGTGCCTTCGCACAGTCCCAACAATCTTCAGTTGTTCAATCTCAACAAAGTTCAAACGCTTATTCTGCAGCATCAACTGCCGGTTCAAGTGTGTCGCAATCTCAGGCGATTGTCTCAAGCGCTCCTGATTATTTTAACACGCAAACTTTAAGTAGCAGCCTGTCTTCTTCTCAGCAATCACTCAGTGCACTCAATTCGATAGCGAGTGGTCAACTGAGCTCCTCGAATGCCGCTTCTATTTTAGCGAGTGCAGTGGCACGGTCACTTGGAGTGTCCCAAGCGTCGGTTCAAAATAGTATAAGCCAACAGTTGAGAAGCGTAGGGCCCGGATCTTCCACGTCCTCTGTCGCTCAAGCAATAGCAAATGGAGTGGCTAACGCAGTTGGAGCATCAGGAACTGGAGTTGCAGGACAAGAACAA
MN704282Aven_2
GCACAACGGGCAGCACAGGAAGCAGCACAACGCGCAGCTCAGCAAGCATCAGCACAACGGGCAGCTCAAGAAGCAGCAGCACAATTGGCAGCTCAGCAAGCAGCAGCACAAAGGGCAGCACAGGAAGCAGCAGCACAACGCGCAGCTCAGCAAGCAGCACAACGCGCAGCACAGCAAGCAGCAGCACAACGGGCCGCTCAGGAAGCGGCAGCTCAACGGGCTGCACAACAAGCAGCAGCTCAAAGGGCAGCGCAGCAAGCAGCAGCTCAAAGAGCAGCTCAGCAAGCAGCAGCTCAAAGCGCAGCTCAGCAAGCAGCAGCTCAACAAGCATCATCCTTCGCACAGTCACAACAATCCTCTGTTGTTCAATCTCAACAAAGTTCAAATGCTTACTCTGCAGCATCAACCTCGGGTTCCAGTGTGTCTCAGTCTCAAGCAATTGTCTCTAGCGCACCTACATATTCCAACACGCAGACGGTCAGTAGCAGCCTGTATTCTTCCCTGCAATCGCAAGCAAGCAGTGCACTAAATTTAATATCGACCGGTCAAGTGAGCTCAACCAGTGCCGCTTCCGCTATAGCGAGTGCCATTGCGCAGTCACTTGGAATTTCCCAGTCAACAGCACAAAATATCATTAGCCAACAATTGAGCAACGTACGAGTCGGATCCTCTACCTCGGCTATAGCTCAAGCCTTATCAAGTGCAATATCTTCCGTAATTGCATCATCAGGATCTTATGTTGCAGGACAGGAGCAATCTATTTCGCAAACCGTATCATCTGCGATTTCTTCTGCTCTATCCCAAATATCAGGACCGGCTCCAGCGCCATCACCGATTTTGGCACCTCGACCACTACCTGCTCCAATACCTGCACCTGCTCCCAGACCAGTCCTCGCACCAGCCGTTTCACAATCTCAGGCAATTTCTGCTTCTTCTTCTTCTTCTCAGGCCACGGCTCAACAAAGTTCTTTCGCACAATCCCAACAATCCTCTGTTGTTCAATCCCAACAATCCTCTGTTATATCTCAACAAAGTTCAAACGCTTACACTGCAGCATCAACCTCGGGTTCCAGTGTGTCTCAGTCTCAAGCAACTGTCTCGAGCGCACCTACATATTCCAACACGCAGACGGTCAGTAGCAGCCTGTATTCTTCCCTTCAATCGCAAGCAAGCAGTGCACTGAATTTAATATCGACCGGTCAAGTGAGCTCAACCAGTGCCGCTTCCGCTATAGCGAGTGCCATTGCGCAGTCACTTGGAATTTCCCAGTCAACAGCACAAAATATCATTAGCCAGCAATTGAGCAACGTACGAGTCGGATCCTCTACCTCGGCTATAGCTCAAGCCTTATCAAGTGCAATATCTTCCGTAATTGCATCGTCAGGATCTTATTCTGCAGGACAGGAGCAATCTATTTCACAAACCGTATCATCTGCGATTTCCTCTGCTCTATCCCAAATATCAGGACCGGCTCCAGCGCCTGCACCGATTTCGGCTCTTGCACCACAACCAACTCCAATTTACGCACCAGCCCCAGTAATTTCCCAAGTTCAGGCAACTTCCTCTTCTTCTCAAACTTTGGCTGAACAGAGTTCTATCACACAGTCTCAGCAGTCTTCCTTTGCTCAAACTCAACAAAGTGCAAACGCTTATTCTGCAGCAGCAGCTCAACAGGCAGCAGCACAACAGGCAGCAGCTCAACAGGCAGCAGCACAACAGGCAGCAGCTCAACAGGCAGCAGCTCAACAGGCAGCAGCACAACAGGCAGCAGCACAACGGGCAGCTCAGCAAGCAGCGGCACAGCAGGCAGCACAACAAGCAGCAGCACAAAGGGCGGCTCAACAAGCAGCAGCACAAAGGGCGGCTCAACAAGCAGCAGCACAAAAAGCGGCTCAACAAGCAGCAGCACAAAGGGCGGCTCAACAAGCAGCAGCACAAAGGGCGGCTCAACAAGCAGCAGCACAAAGGGCGGCTCAACAAGCAGCAGCACAAAGGGCGGCTCAACAAGCAGCAGCACAAAGGGCGGCTCAACAAGCAGCAGCACAAAGGGCTGCTCAACAAGCAGCAGCACAACGGGCAGCTCAGGAAGCAGCAGCTCAAAGGGCAGCTCAGGAAGCAGCAGCTCAAAGGGCTGCTCAGCAAGCAGCGGCACAAAGGGCAGCACAACAAGCAGCGGCTCAAAGGGCAGCACAACAAGCAGCAGCTCAAAGGGCAGCTCAACAAGCAGCAGCTCAAAGGGCAGCCCAGCAGGCGGCAGCTCAACAGGCAGCACAACAAGCAGCAGCACAAAGGGCAGCGCAGCAGGCGGCCGCTCAAAGGGCAGCGCAGCAAGCAGCAGCTCAAAGAGCAGCTCAGCGAGCAGCAGCTCAACAAGCATCATCCTTCGCACAGTCACAACAATCCTCTGTTGTTCAATCTCAACAAAGTTCAAATGCTTACTCTGCAGCATCAACCTCGGGTTCCAGTGTGTCTCAGTCTCAAGCAATTGTCTCTAGCGCACCTACATATTCCAACACGCAGACAGTCAGTAGCAGCCTGTATTCTTCCCTGCAATCGCAAGCAAGCAGTGCACTAAATTTAATATCGACCGGTCAAGTGAGCTCAACCAGTGCCGCTTCCGCTATAGCGAGTGCCATTGCGCAGTCACTTGGAATTTCCCAGTCAACAGCACAAAATATCATTAGCCAACAATTGAGCAACGTACGAGTCGGATCCTCTACCTCGGCTATAGCTCAAGCCTTATCAAGTGCAATATCTTCCGTAATTGCATCATCAGGATCTTATGTTGCAGGACAGGAGCAATCTATTTCGCAAACCGTATCATCTGCGATTTCTTCTGCTCTATCCCAAATATCAGGACCGGCTCCAGCGCCATCACCGATTTCGGCACCTCGACCACTACCTGCTCCAATACCTGCACCTGCTCCACGACCAGTCCTCGCACCACAAACTGCTTCAGTCACTAGTTACGCACCAGTTGTTTCACAATCTCAGGCAATTTCTTCTTCTCAGGCCTCGGCTCAACAGAGTTCTTTCGCACAATCCCAACAGTCCTCTGTTGTTCAATCCCAACAATCCTCTGTTCAATCTCAACAAAGTTCAAACGCGTATTCTGCAGCATCAACCTCGGGTTCCAGTGTGTCTCAGTCTCAAGCAATTGTCTCTAGCGCACCTACATATTCCAACACGCAGACAGTCAGTAGCAGCCTGTATTCTTCCCTGCAATCGCAAGCAAGCAGTGCACTAAATTTAATATCGACCGGTCAAGTGAGCTCAACCAGTGCCGCTTCCGCTATAGCGAGTGCCATTGCGCAGTCACTTGGAATTTCCCAGTCAACAGCACAAAATATCATTAGCCAACAATTGAGCAAC

二:零假设

## tree文件
5 1
((MH376748Aven,KY398016Aarg),(LC570228Osyb,FJ973621Lhes) ,MN704282Aven_2);

codeml.ctl

      seqfile = /home/spider/project/yuantao/test3/10_positive_selection/nuc.txt * sequence data filename
     treefile = /home/spider/project/yuantao/test3/10_positive_selection/frist.tree      * tree structure file name
      outfile = /home/spider/project/yuantao/test3/10_positive_selection/result0.txt           * main result file name

        noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
      verbose = 1  * 0: concise; 1: detailed, 2: too much
      runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
                   * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

      seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
    CodonFreq = 2  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table

*        ndata = 10
        clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
   aaRatefile = dat/jones.dat  * only used for aa seqs with model=empirical(_F)
                   * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

        model = 0
                   * models for codons:
                       * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
                   * models for AAs or codon-translated AAs:
                       * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
                       * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

      NSsites = 0  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
                   * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
                   * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
                   * 13:3normal>0

        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
        Mgene = 0
                   * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
                   * AA: 0:rates, 1:separate

    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
        kappa = 2  * initial or fixed kappa
    fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate 
        omega = .4 * initial or fixed omega, for codons or codon-based AAs

    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
        alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
       Malpha = 0  * different alphas for genes
        ncatG = 8  * # of categories in dG of NSsites models

        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 1  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

   Small_Diff = .5e-6
    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
*  fix_blength = 1  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional
       method = 0  * Optimization method 0: simultaneous; 1: one branch a time

* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.
(END)

三:替代假设

5 1
((MH376748Aven,KY398016Aarg),(LC570228Osyb,FJ973621Lhes) $1,MN704282Aven_2);
      seqfile = /home/spider/project/yuantao/test3/10_positive_selection/nuc.txt * sequence data filename
     treefile = /home/spider/project/yuantao/test3/10_positive_selection/frist.tree      * tree structure file name
      outfile = /home/spider/project/yuantao/test3/10_positive_selection/result2.txt           * main result file name

        noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
      verbose = 1  * 0: concise; 1: detailed, 2: too much
      runmode = 0  * 0: user tree;  1: semi-automatic;  2: automatic
                   * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

      seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
    CodonFreq = 2  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table

*        ndata = 10
        clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
   aaRatefile = dat/jones.dat  * only used for aa seqs with model=empirical(_F)
                   * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

        model = 2
                   * models for codons:
                       * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
                   * models for AAs or codon-translated AAs:
                       * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
                       * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

      NSsites = 0  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
                   * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
                   * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
                   * 13:3normal>0

        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
        Mgene = 0
                   * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
                   * AA: 0:rates, 1:separate

    fix_kappa = 0  * 1: kappa fixed, 0: kappa to be estimated
        kappa = 2  * initial or fixed kappa
    fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate 
        omega = .4 * initial or fixed omega, for codons or codon-based AAs

    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
        alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
       Malpha = 0  * different alphas for genes
        ncatG = 8  * # of categories in dG of NSsites models

        getSE = 0  * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 1  * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

   Small_Diff = .5e-6
    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
*  fix_blength = 1  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional
       method = 0  * Optimization method 0: simultaneous; 1: one branch a time

* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt., 
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt., 
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.

四:运行零假设和替代假设的ctl文件

/home/spider/project/yuantao/soft/paml4.9j/bin/codeml /home/spider/project/yuantao/soft/paml4.9j/codeml.ctl

会获得两个结果文件:result0.txt和result2.txt,其中最主要的看Likehood radio test(lnL)值和omeag(w )值,如下:
其中零假设(1个omega值)

lnL0(ntime:  7  np0:  9): -21384.472055      +0.000000
omega (dN/dS) =  0.86618

替代假设(2个omega值)

lnL2(ntime:  7  np2: 10): -21376.996759      +0.000000
w (dN/dS) for branches:  0.05555 3.45230

对于inL值,可以用R进行一个p检验;
其中lnL2-lnL0符合Chi^2分布,df=np2-np0,从而得到显著性P值。

pchisq(-21376.996759+21384.472055,10-9,lower.tail = FALSE)
[1] 0.006255128

结果为0.006255128<10%,表示在10%的significance的情况下拒绝零假设,接受替代假设。

w (dN/dS) for branches:  0.05555 3.45230

所以从替代假设的omega值中,可以看到PiSp2的dN/dS值要大于PiSp1的dN/dS值,PiSp1<1为negative selection,PiSp2>1为positiveselection

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