MalacoWiki

wiki of malacology

TIGER

使用TIGER软件可以确定快速演化位点,但是,它并不能移除这些位点。本文将介绍如何使用TIGER识别位点。这个软件的作用就是可以让导致序列饱和度过高的位点显现出来。

TIGER的使用

  • 下载TIGER后解压即可。目前下载似乎没有官方途径,可以联系我发送一个copy。
  • 解压后我是将软件存至C:\tiger,所以使用很简单,准备好fas文件,放置于C:\tiger\dist
  • Win+R调出运行,输入cmd,之后输入cd C:\tiger\dist回车 输入文件命令为tiger –in [你的输入文件/your input file].fas
  • 输出命令为tiger -in [你的输入文件/your input file].fas > [你的输出文件/your output file].nexus
  • 更改bin的数量tiger –in input.fas –b [你要更改到的bin数量]

文件示例

输入文件

>Aquifex 1273 bp
CTCAGCGCGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGTGCGCAGAGCGGCAAACG
GGTGAGTAACACGTGGGTAACCTACCCCCAGGAGGGGGATAACCCCGGGAAACCGGGGCT
AATACCCCATAAAGCCGATGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
CCAAGCCTATGACGGGTAGCCGGCCTGAGAGGGTGGCCGGCCACAGCGGGACTGAGACAC
GGCCCGCACCCCTACGGGGGGCAGCAGTGGGGAATCGTGGGCAATGGGCGAAAGCCTGAC
CCCGCGACGCCGCGTGGGGGAAGAAGCCCTGCGGGGTGTAAACCCCTGTCGGGGGGGACG
TGACGGTACCCCCAGAGGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
CCCGAGCGTTGCGCGAAGTCACTGGGCGTAAAGCGTCCGCAGCCGGTCGGGTAAGCGGGA
TGTCAAAGCCCACGGCTCAACCGTGGAATGGCATCCCGAACTGCCCGACTTGAGGCACGC
CCGGGCAGGCGGAATTCCCGGGGTAGCGGTGAAATGCGTAGATCTCGGGAGGAACACCGA
AGGGGAAGCCAGCCTGCTGGGGCTGTCCTGACGGTCAGGGACGAAAGCCGGGGGAGCGAA
CCGGATTAGATACCCGGGTAGTCCCGGCCGTAAACCATGGGCGCTAGGGCTGCAGGCTCG
CAGCTAACGCGTTAAGCGCCCCGCCTGGGGAGTACGGGCGCAAGCCTGAAACTCAAAGGA
ATTGGCGGGGGCCCGCACAACCGGTGGAGCGTCTGGTTCAATTCGATGCTAACCGAAGAA
CCTTACCCGGGCTTGACATGGCACAGGTGGTGCATGGCCGTCGTCAGCTCGTGTCGTGAG
ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCTGAGCACTCTAGG
GGGACCGCCGGCGCCGGAGGAAGGGGGGGATGACGTCAGGTCAGTATGCCCTTTATGCCC
GGGGCCACACAGGCGCTACAGTGGCCGGGACAATGGGAAGCGACCCCGCAAGGGGGAGCT
AATCCCAGAAACCCGGTCATGGTGCGGATTGGGGGCTGAAACTCGCCCCCATGAAGCCGG
AATCGGTAGTAACGGGGTATCAGCGATGTCCCCGTGAATACGTTCTCGGGCCTTGCACAC
ACCGCCCGTCACGCCACGGAAGTCGGTCCGGCCGGAAGGACTGGGGCGAAGTCGTAACAA
GGTAGCCGTAGGG
>Deinococcus 1273 bp
CTCAGGGTGAACGCTGGCGGCGTGCTTAAGACATGCAAGTCGAACGCGGAGTGGCGCACG
GGTGAGTAACACGTAACTGACCTACCCAGAAGTCATGAATAACTGGCCGAAAGGTCAGCT
AATACGTGATGTGGTGGATGGGGTTGCGTTCCATCAGCTGGTTGGTGGGGTAAAGGCCTA
CCAAGGCGACGACGGATAGCCGGCCTGAGAGGGTGGCCGGCCACAGGGGCACTGAGACAC
GGGTCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCACAATGGGCGCAAGCCTGAT
GGAGCGACGCCGCGTGAGGGATGAAGGTTTTCGGATCGTAAACCTCTGAATCTGGG-ACG
TGACGGTACCAGAGTAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
TGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGATATTTAAGTCTGG
TTTTAAAGACCGAGGCTCAACCTCGGGAGTGGACTGGATACTGGATGTCTTGACCTCTGG
AGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAA
TGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAA
CCGGATTAGATACCCGGGTAGTCCACACCCTAAACGATGTACGTTGGCTAATGCTTGGCG
AAGCTAACGCGATAAACGTACCGCCTGGGAAGTACGGCCGCAAGGTTGAAACTCAAAGGA
ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
CCTTACCAGGTCTTGACATGACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAG
ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCTTCCAGTTGCCGGGCACTCTGGA
GGGACTGCCTGTGCAGGAGGAAGGCGGGGATGACGTCTAGTCAGCATGGTCCTTACGTCC
TGGGCTACACACGTGCTACAATGGATAGGACAACGCGCAGCAAACATGTGAGTGTAAGCG
AATCGCTGAAACCTATCCCCAGTTCAGATCGGAGTCTGCAACTCGACTCCGTGAAGTTGG
AATCGCTAGTAATCGCGGGTCAGC-ATACCGCGGTGAATACGTTCCCGGGCCTTGTACAC
ACCGCCCGTCACACCATGGGAGTAGATTGCAGTTGAAAGACTGGGGTGAAGTCGTAACAA
GGTAACTGTACCG
>Thermotoga 1273 bp
CTCAGGGTGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAGCGGGGAGCGGCGGACG
GGTGAGTAACACGTGGGTAACCTGCCCTCCGGAGGGGGATAACCAGGGGAAACCCTGGCT
AATACCCCATACGCTCGAGGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
CCAAGCCGACGACGGGTAGCCGGCCTGAGAGGGTGGTCGGCCACAGGGGCACTGAGACAC
GGGCCCCACTCCTACGGGAGGCAGCAGTGGGGAATCTTGGACAATGGGGGAAACCCTGAT
CCAGCGACGCCGCGTGCGGGACGAAGCCCTTCGGGGTGTAAACCGCTGTGGCGGGGGAAG
TGACGGTACCCCGCTAGGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGG
GGCAAGCGTTACCCGGATTTACTGGGCGTAAAGGGGGCGTAGGCGGCCTGGTGTGTCGGA
TGTGAAATCCCACGGCTCAACCGTGGGGCTGCATCCGAAACTACCAGGCTTGGGGGCGGT
AGAGGGAGACGGAACTGCCGGTGTAGGGGTGAAATCCGTAGATATCGGCAGGAACGCCGG
TGGGGAAGCCGGTCTCCTGGGCCGACCCCGACGCTGAGGCCCGAAAGCCAGGGGAGCAAA
CCGGATTAGATACCCGGGTAGTCCTGGCTGTAAACGATGCCCACTAGGTGTTCCGTGCTG
AAGCTAACGCGTTAAGTGGGCCGCCTGGGGAGTACGCCCGCAAGGGTGAAACTCAAAGGA
ATTGACGGGGGCCCGCACAAGCGGTGGAGCGTGTGGTTTAATTGGATGCTAAGCCAAGAA
CCTTACCAGGGCTTGACATGGCACAGGTGGTGCACGGCCGTCGTCAGCTCGTGCCGTGAG
GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCCGGGCACTCTAGG
GGGACTGCCGGCGCCGGAGGAAGGAGGGGATGACGTCAGGTACTCGTGCCCCTTATGCCC
TGGGCGACACACGCGCTACAATGGGCGGTACAATGGGTTGCGACCCCGCGAGGGGGAGCC
AATCCC-CAAAGCCGCCCTCAGTTCGGATCGCAGGCTGCAACCCGCCTGCGTGAAGCCGG
AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
ACCGCCCGTCACGCCACCCGAGTCGGGGGCTCCCGAAGGAGGGGGGCGAAGTCGTAACAA
GGTAGCCGTACCG
>Bacillus 1273 bp
CTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGACAGCGGCGGACG
GGTGAGTAACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCT
AATACCGGATGGTTGTGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCA
CCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACAC
GGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGAC
GGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAG
TGACGGTACCTAACCAGGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
GGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGA
TGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGA
AGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAG
TGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAA
CAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTTAGTGCTG
CAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGA
ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
CCTTACCAGGTCTTGACATCTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAG
ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCGGGCACTCTAAG
GTGACTGCCGGTGCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACC
TGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCAGCGAAACCGCGAGGTTAAGCC
AATCCCACAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGG
AATCGCTAGTAATCGCGGATCAGC-ATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
ACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGGATTGGGGTGAAGTCGTAACAA
GGTAGCCGTATCG
>Thermus 1273 bp
CTCAGGGTGAACGCTGGCGGCGTGCCTAAGACATGCAAGTCGTGCGGGCAGCGGCGGACG
GGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGGGGACAACCCGGGGAAACTCGGGCT
AATCCCCCATGTGGACGATGGGCCCGCGTCCCATCAGCTAGTTGGTGGGGTAATGGCCCA
CCAAGGCGACGACGGGTAGCCGGTCTGAGAGGATGGCCGGCCACAGGGGCACTGAGACAC
GGGCCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGCAAGCCTGAC
GGAGCGACGCCGCTTGGAGGAAGAAGCCCTTCGGGGTGTAAACTCCTGAACCCGGG-ACG
TGACGGTACCGGGGTAAGCGCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
CGCGAGCGTTACCCGGATTCACTGGGCGTAAAGGGCGTGTAGGCGGCCTGGGGCGTCCCA
TGTGAAAGACCACGGCTCAACCGTGGGGGAGCGTGGGATACGCTCAGGCTAGACGGTGGG
AGAGGGTGGTGGAATTCCCGGAGTAGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGA
TGGCGAAGGCAGCCACCTGGTCCACCCGTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAA
CCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGCGCGCTAGGTCTTGGGGGCCG
AAGCTAACGCGTTAAGCGCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGA
ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
CCTTACCAGGCCTTGACATGGCACAGGTGCTGCATGGCCGTCGTCAGCTCGTGCCGTGAG
GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCGCCGTTAGTTGCCGGGCACTCTAAC
GGGACTGCCCGCGCGGGAGGAAGGAGGGGACGACGTCTGGTCAGCATGGCCCTTACGGCC
TGGGCGACACACGTGCTACAATGCCC--TACAAAGCGATGCCACCCGGCAACGGGGAGCT
AATCGCAAAAAGGTGGGCCCAGTTCGGATTGGGGTCTGCAACCCGACCCCATGAAGCCGG
AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
ACCGCCCGTCACGCCATGGGAGCGGGCTCTACCCGAAGGACTGGGGCGAAGTCGTAACAA
GGTAGCTGTACCG

输出文件

#NEXUS

[This file contains data that has been analysed for site specific rates]
[using TIGER, developed by Carla Cummins in the laboratory of]
[Dr James McInerney, National University of Ireland, Maynooth]


[Histograms of number of sites in each category:]
[Bin1	|============================================================ |833  ]
[Bin2	|                                                             |0    ]
[Bin3	|                                                             |0    ]
[Bin4	|                                                             |0    ]
[Bin5	|                                                             |0    ]
[Bin6	|=========                                                    |116  ]
[Bin7	|=======                                                      |87   ]
[Bin8	|======                                                       |72   ]
[Bin9	|=======                                                      |96   ]
[Bin10	|=====                                                        |69   ]






BEGIN TAXA;
	Dimensions NTax =  5 ;
	TaxLabels  Aquifex1273bp        Deinococcus1273bp    Thermotoga1273bp     Bacillus1273bp       Thermus1273bp        ;
END;

BEGIN CHARACTERS;
	Dimensions nchar =  1273 ;
	Format datatype =  DNA  gap = - interleave;
Matrix

Aquifex1273bp       	CTCAGCGCGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGTGCGCAGAGCGGCAAACG
Deinococcus1273bp   	CTCAGGGTGAACGCTGGCGGCGTGCTTAAGACATGCAAGTCGAACGCGGAGTGGCGCACG
Thermotoga1273bp    	CTCAGGGTGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAGCGGGGAGCGGCGGACG
Bacillus1273bp      	CTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGACAGCGGCGGACG
Thermus1273bp       	CTCAGGGTGAACGCTGGCGGCGTGCCTAAGACATGCAAGTCGTGCGGGCAGCGGCGGACG
[Bin Numbers        	111116791111111111111111161119111111111111961119111611161111]
[                    	                                              0 0       0   ]


Aquifex1273bp       	GGTGAGTAACACGTGGGTAACCTACCCCCAGGAGGGGGATAACCCCGGGAAACCGGGGCT
Deinococcus1273bp   	GGTGAGTAACACGTAACTGACCTACCCAGAAGTCATGAATAACTGGCCGAAAGGTCAGCT
Thermotoga1273bp    	GGTGAGTAACACGTGGGTAACCTGCCCTCCGGAGGGGGATAACCAGGGGAAACCCTGGCT
Bacillus1273bp      	GGTGAGTAACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCT
Thermus1273bp       	GGTGAGTAACGCGTGGGTGACCTACCCGGAAGAGGGGGACAACCCGGGGAAACTCGGGCT
[Bin Numbers        	111111111171116661811119117197816896161711181966111169116111]
[                    	                           0                0         00    ]


Aquifex1273bp       	AATACCCCATAAAGCCGATGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
Deinococcus1273bp   	AATACGTGATGTGGTGGATGGGGTTGCGTTCCATCAGCTGGTTGGTGGGGTAAAGGCCTA
Thermotoga1273bp    	AATACCCCATACGCTCGAGGGGCCCGCGGCCCATCAGGTAGTTGGTGGGGTAACGGCCCA
Bacillus1273bp      	AATACCGGATGGTTGTGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCA
Thermus1273bp       	AATCCCCCATGTGGACGATGGGCCCGCGTCCCATCAGCTAGTTGGTGGGGTAATGGCCCA
[Bin Numbers        	111716981181991911711766611186711171181611111117111119111761]
[                    	           0  0                                             ]


Aquifex1273bp       	CCAAGCCTATGACGGGTAGCCGGCCTGAGAGGGTGGCCGGCCACAGCGGGACTGAGACAC
Deinococcus1273bp   	CCAAGGCGACGACGGATAGCCGGCCTGAGAGGGTGGCCGGCCACAGGGGCACTGAGACAC
Thermotoga1273bp    	CCAAGCCGACGACGGGTAGCCGGCCTGAGAGGGTGGTCGGCCACAGGGGCACTGAGACAC
Bacillus1273bp      	CCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACAC
Thermus1273bp       	CCAAGGCGACGACGGGTAGCCGGTCTGAGAGGATGGCCGGCCACAGGGGCACTGAGACAC
[Bin Numbers        	111118191611717611111177111111117117911111111791191111111111]
[                    	                                                            ]


Aquifex1273bp       	GGCCCGCACCCCTACGGGGGGCAGCAGTGGGGAATCGTGGGCAATGGGCGAAAGCCTGAC
Deinococcus1273bp   	GGGTCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCACAATGGGCGCAAGCCTGAT
Thermotoga1273bp    	GGGCCCCACTCCTACGGGAGGCAGCAGTGGGGAATCTTGGACAATGGGGGAAACCCTGAT
Bacillus1273bp      	GGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGAC
Thermus1273bp       	GGGCCCCACTCCTACGGGAGGCAGCAGTTAGGAATCTTCCGCAATGGGCGCAAGCCTGAC
[Bin Numbers        	119619711611111111611111111198111111618811111117718117711111]
[                    	                                        0                  0]


Aquifex1273bp       	CCCGCGACGCCGCGTGGGGGAAGAAGCCCTGCGGGGTGTAAACCCCTGTCGGGGGGGACG
Deinococcus1273bp   	GGAGCGACGCCGCGTGAGGGATGAAGGTTTTCGGATCGTAAACCTCTGAATCTGGG-ACG
Thermotoga1273bp    	CCAGCGACGCCGCGTGCGGGACGAAGCCCTTCGGGGTGTAAACCGCTGTGGCGGGGGAAG
Bacillus1273bp      	GGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAG
Thermus1273bp       	GGAGCGACGCCGCTTGGAGGAAGAAGCCCTTCGGGGTGTAAACTCCTGAACCCGGG-ACG
[Bin Numbers        	886117111111171117711111118881611188811111771111819997118191]
[                    	                0    0                      0    0          ]


Aquifex1273bp       	TGACGGTACCCCCAGAGGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
Deinococcus1273bp   	TGACGGTACCAGAGTAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
Thermotoga1273bp    	TGACGGTACCCCGCTAGGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGG
Bacillus1273bp      	TGACGGTACCTAACCAGGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGT
Thermus1273bp       	TGACGGTACCGGGGTAAGCGCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGG
[Bin Numbers        	111111111119119181619111171111811111111111111111111111181119]
[                    	          0 00     0                                        ]


Aquifex1273bp       	CCCGAGCGTTGCGCGAAGTCACTGGGCGTAAAGCGTCCGCAGCCGGTCGGGTAAGCGGGA
Deinococcus1273bp   	TGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGATATTTAAGTCTGG
Thermotoga1273bp    	GGCAAGCGTTACCCGGATTTACTGGGCGTAAAGGGGGCGTAGGCGGCCTGGTGTGTCGGA
Bacillus1273bp      	GGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGA
Thermus1273bp       	CGCGAGCGTTACCCGGATTCACTGGGCGTAAAGGGCGTGTAGGCGGCCTGGGGCGTCCCA
[Bin Numbers        	161911111197611611191711111111111619981911611118198799166976]
[                    	0                0                            0 0           ]


Aquifex1273bp       	TGTCAAAGCCCACGGCTCAACCGTGGAATGGCATCCCGAACTGCCCGACTTGAGGCACGC
Deinococcus1273bp   	TTTTAAAGACCGAGGCTCAACCTCGGGAGTGGACTGGATACTGGATGTCTTGACCTCTGG
Thermotoga1273bp    	TGTGAAATCCCACGGCTCAACCGTGGGGCTGCATCCGAAACTACCAGGCTTGGGGGCGGT
Bacillus1273bp      	TGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGA
Thermus1273bp       	TGTGAAAGACCACGGCTCAACCGTGGGGGAGCGTGGGATACGCTCAGGCTAGACGGTGGG
[Bin Numbers        	161111178119611111111169119191767698668117999171117178919111]
[                    	   0                       0 0               0 0       0 0 0]


Aquifex1273bp       	CCGGGCAGGCGGAATTCCCGGGGTAGCGGTGAAATGCGTAGATCTCGGGAGGAACACCGA
Deinococcus1273bp   	AGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAA
Thermotoga1273bp    	AGAGGGAGACGGAACTGCCGGTGTAGGGGTGAAATCCGTAGATATCGGCAGGAACGCCGG
Bacillus1273bp      	AGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAG
Thermus1273bp       	AGAGGGTGGTGGAATTCCCGGAGTAGCGGTGAAATGCGCAGATACCGGGAGGAACGCCGA
[Bin Numbers        	666111181811117171971911117111161117117111768791711111191189]
[                    	     00 0                                                   ]


Aquifex1273bp       	AGGGGAAGCCAGCCTGCTGGGGCTGTCCTGACGGTCAGGGACGAAAGCCGGGGGAGCGAA
Deinococcus1273bp   	TGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAA
Thermotoga1273bp    	TGGGGAAGCCGGTCTCCTGGGCCGACCCCGACGCTGAGGCCCGAAAGCCAGGGGAGCAAA
Bacillus1273bp      	TGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAA
Thermus1273bp       	TGGCGAAGGCAGCCACCTGGTCCACCCGTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAA
[Bin Numbers        	611811118198181111111699119871111616111991111116891111111911]
[                    	            0 00    0   00                                  ]


Aquifex1273bp       	CCGGATTAGATACCCGGGTAGTCCCGGCCGTAAACCATGGGCGCTAGGGCTGCAGGCTCG
Deinococcus1273bp   	CCGGATTAGATACCCGGGTAGTCCACACCCTAAACGATGTACGTTGGCTAATGCTTGGCG
Thermotoga1273bp    	CCGGATTAGATACCCGGGTAGTCCTGGCTGTAAACGATGCCCACTAGGTGTTCCGTGCTG
Bacillus1273bp      	CAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTTAGTGCTG
Thermus1273bp       	CCGGATTAGATACCCGGGTAGTCCACGCCCTAAACGATGCGCGCTAGGTCTTGGGGGCCG
[Bin Numbers        	171111111111111711111111986178111116111117761676616691696191]
[                    	                                       00        0   0   0  ]


Aquifex1273bp       	CAGCTAACGCGTTAAGCGCCCCGCCTGGGGAGTACGGGCGCAAGCCTGAAACTCAAAGGA
Deinococcus1273bp   	AAGCTAACGCGATAAACGTACCGCCTGGGAAGTACGGCCGCAAGGTTGAAACTCAAAGGA
Thermotoga1273bp    	AAGCTAACGCGTTAAGTGGGCCGCCTGGGGAGTACGCCCGCAAGGGTGAAACTCAAAGGA
Bacillus1273bp      	CAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGA
Thermus1273bp       	AAGCTAACGCGTTAAGCGCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGA
[Bin Numbers        	911111111176111677111111111116111111791111119111111111111111]
[                    	                  00                         0              ]


Aquifex1273bp       	ATTGGCGGGGGCCCGCACAACCGGTGGAGCGTCTGGTTCAATTCGATGCTAACCGAAGAA
Deinococcus1273bp   	ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
Thermotoga1273bp    	ATTGACGGGGGCCCGCACAAGCGGTGGAGCGTGTGGTTTAATTGGATGCTAAGCCAAGAA
Bacillus1273bp      	ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
Thermus1273bp       	ATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAA
[Bin Numbers        	111161111111111111116111111111816111116111171181181861711111]
[                    	                                                            ]


Aquifex1273bp       	CCTTACCCGGGCTTGACATGGCACAGGTGGTGCATGGCCGTCGTCAGCTCGTGTCGTGAG
Deinococcus1273bp   	CCTTACCAGGTCTTGACATGACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAG
Thermotoga1273bp    	CCTTACCAGGGCTTGACATGGCACAGGTGGTGCACGGCCGTCGTCAGCTCGTGCCGTGAG
Bacillus1273bp      	CCTTACCAGGTCTTGACATCTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAG
Thermus1273bp       	CCTTACCAGGCCTTGACATGGCACAGGTGCTGCATGGCCGTCGTCAGCTCGTGCCGTGAG
[Bin Numbers        	111111161191111111179711111118111171178111111111111119111111]
[                    	                                                            ]


Aquifex1273bp       	ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCTGAGCACTCTAGG
Deinococcus1273bp   	ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCTTCCAGTTGCCGGGCACTCTGGA
Thermotoga1273bp    	GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGCCCCTAGTTGCCGGGCACTCTAGG
Bacillus1273bp      	ATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCGGGCACTCTAAG
Thermus1273bp       	GTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCCGCCGTTAGTTGCCGGGCACTCTAAC
[Bin Numbers        	911111111111111111111111111111111871789161111116161111111619]
[                    	                                       0                  0 ]


Aquifex1273bp       	GGGACCGCCGGCGCCGGAGGAAGGGGGGGATGACGTCAGGTCAGTATGCCCTTTATGCCC
Deinococcus1273bp   	GGGACTGCCTGTGCAGGAGGAAGGCGGGGATGACGTCTAGTCAGCATGGTCCTTACGTCC
Thermotoga1273bp    	GGGACTGCCGGCGCCGGAGGAAGGAGGGGATGACGTCAGGTACTCGTGCCCCTTATGCCC
Bacillus1273bp      	GTGACTGCCGGTGCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACC
Thermus1273bp       	GGGACTGCCCGCGCGGGAGGAAGGAGGGGACGACGTCTGGTCAGCATGGCCCTTACGGCC
[Bin Numbers        	171116111918119111111111111111711111188717796711861611181111]
[                    	                        0                                0  ]


Aquifex1273bp       	GGGGCCACACAGGCGCTACAGTGGCCGGGACAATGGGAAGCGACCCCGCAAGGGGGAGCT
Deinococcus1273bp   	TGGGCTACACACGTGCTACAATGGATAGGACAACGCGCAGCAAACATGTGAGTGTAAGCG
Thermotoga1273bp    	TGGGCGACACACGCGCTACAATGGGCGGTACAATGGGTTGCGACCCCGCGAGGGGGAGCC
Bacillus1273bp      	TGGGCTACACACGTGCTACAATGGACAGAACAAAGGGCAGCGAAACCGCGAGGTTAAGCC
Thermus1273bp       	TGGGCGACACACGTGCTACAATGCCC--TACAAAGCGATGCCACCCGGCAACGGGGAGCT
[Bin Numbers        	611111111116181111116117169711111118119119187691691767881111]
[                    	     0                  0   0    0   0                     0]


Aquifex1273bp       	AATCCCAGAAACCCGGTCATGGTGCGGATTGGGGGCTGAAACTCGCCCCCATGAAGCCGG
Deinococcus1273bp   	AATCGCTGAAACCTATCCCCAGTTCAGATCGGAGTCTGCAACTCGACTCCGTGAAGTTGG
Thermotoga1273bp    	AATCCC-CAAAGCCGCCCTCAGTTCGGATCGCAGGCTGCAACCCGCCTGCGTGAAGCCGG
Bacillus1273bp      	AATCCCACAAATCTGTTCTCAGTTCGGATCGCAGTCTGCAACTCGACTGCGTGAAGCTGG
Thermus1273bp       	AATCGCAAAAAGGTGGGCCCAGTTCGGATTGGGGTCTGCAACCCGACCCCATGAAGCCGG
[Bin Numbers        	111181111111786111166116161119199181116111911819919111116811]
[                    	      00   0   00 0                                         ]


Aquifex1273bp       	AATCGGTAGTAACGGGGTATCAGCGATGTCCCCGTGAATACGTTCTCGGGCCTTGCACAC
Deinococcus1273bp   	AATCGCTAGTAATCGCGGGTCAGC-ATACCGCGGTGAATACGTTCCCGGGCCTTGTACAC
Thermotoga1273bp    	AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
Bacillus1273bp      	AATCGCTAGTAATCGCGGATCAGC-ATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
Thermus1273bp       	AATCGCTAGTAATCGCGGATCAGCCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACAC
[Bin Numbers        	111116111111661616611111111661616111111111111611111111161111]
[                    	                        0                                   ]


Aquifex1273bp       	ACCGCCCGTCACGCCACGGAAGTCGGTCCGGCCGGAAGGACTGGGGCGAAGTCGTAACAA
Deinococcus1273bp   	ACCGCCCGTCACACCATGGGAGTAGATTGCAGTTGAAAGACTGGGGTGAAGTCGTAACAA
Thermotoga1273bp    	ACCGCCCGTCACGCCACCCGAGTCGGGGGCTCCCGAAGGAGGGGGGCGAAGTCGTAACAA
Bacillus1273bp      	ACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGGATTGGGGTGAAGTCGTAACAA
Thermus1273bp       	ACCGCCCGTCACGCCATGGGAGCGGGCTCTACCCGAAGGACTGGGGCGAAGTCGTAACAA
[Bin Numbers        	111111111111811187961171769119966111161197111181111111111111]
[                    	                       0   00    0                          ]


Aquifex1273bp       	GGTAGCCGTAGGG
Deinococcus1273bp   	GGTAACTGTACCG
Thermotoga1273bp    	GGTAGCCGTACCG
Bacillus1273bp      	GGTAGCCGTATCG
Thermus1273bp       	GGTAGCTGTACCG
[Bin Numbers        	1111618111961]
[                    	             ]




;
END;

BEGIN PAUP;
	Charset Bin1 =  1 2 3 4 5 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 27 28 29 31 32 33 34 35 36 37 38 39 40 41 42 45 46 50 51 53 54 55 58 59 60 61 62 63 64 65 66 67 68 69 70 72 73 74 78 80 81 82 83 85 86 92 97 99 101 102 103 109 110 111 112 118 119 120 121 122 123 125 129 130 137 138 140 141 146 147 148 152 153 154 156 157 159 161 162 163 164 165 166 167 169 170 171 172 173 175 176 177 180 181 182 183 184 185 187 189 191 192 194 197 198 199 200 201 202 205 206 207 208 209 210 211 212 214 215 218 219 220 221 222 223 224 225 228 229 231 232 233 234 235 236 237 238 239 240 241 242 245 248 249 251 252 253 254 255 256 257 258 260 261 262 263 264 265 266 267 268 271 272 273 274 275 276 278 282 283 284 285 286 287 290 292 293 296 297 298 299 304 305 307 308 309 310 311 312 313 315 316 320 321 323 324 325 326 330 332 333 334 338 339 340 341 342 346 347 348 355 356 358 360 361 362 363 364 365 366 367 368 369 370 376 378 382 383 384 385 387 388 389 390 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 417 418 419 423 425 426 427 428 429 430 434 435 437 439 441 443 444 445 446 447 448 449 450 451 452 453 455 459 461 462 464 465 466 475 481 483 485 486 487 490 491 494 495 496 497 498 499 500 501 502 505 506 520 521 529 530 532 539 544 545 551 552 553 554 556 558 561 563 564 565 566 568 569 570 571 573 574 575 577 578 580 581 582 588 590 591 592 593 594 595 597 598 602 603 605 606 607 608 610 617 618 619 620 630 631 632 633 635 637 638 639 642 643 644 645 646 647 651 652 653 654 655 656 657 659 660 661 663 664 665 666 667 668 669 670 671 672 673 674 675 677 678 679 680 681 682 683 684 688 691 692 693 694 695 697 698 699 705 720 722 723 724 725 726 727 728 729 730 733 734 735 741 742 743 744 745 746 747 748 749 751 752 753 754 755 756 759 760 761 762 763 764 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 802 803 804 805 806 807 808 809 810 812 814 815 816 817 818 820 821 822 823 825 826 828 829 831 834 836 837 838 839 840 841 842 843 844 845 846 847 849 850 852 853 854 855 856 857 858 859 863 864 865 866 867 868 869 871 872 873 874 876 877 880 881 882 883 884 885 886 887 888 889 890 891 892 893 895 896 897 898 899 900 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 936 942 943 944 945 946 947 949 951 952 953 954 955 956 957 961 963 964 965 967 968 969 971 973 974 976 977 978 979 980 981 982 983 984 986 987 988 989 990 992 993 994 995 996 997 1001 1007 1008 1011 1013 1014 1015 1017 1019 1020 1022 1023 1024 1025 1027 1028 1029 1030 1031 1033 1035 1036 1037 1038 1039 1040 1042 1043 1050 1051 1052 1053 1055 1057 1060 1061 1063 1068 1071 1077 1078 1079 1081 1082 1083 1084 1086 1089 1090 1091 1098 1102 1103 1105 1107 1108 1109 1111 1114 1116 1117 1118 1120 1121 1122 1124 1125 1127 1130 1132 1133 1134 1135 1136 1139 1140 1141 1142 1143 1144 1145 1147 1148 1149 1150 1151 1152 1155 1157 1160 1161 1162 1163 1164 1166 1167 1170 1172 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1187 1188 1189 1190 1191 1192 1193 1194 1195 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1214 1215 1216 1221 1222 1235 1236 1237 1239 1240 1243 1244 1245 1246 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1266 1268 1269 1270 1273;
	Charset Bin6 =  6 26 44 52 56 75 76 77 93 96 98 107 108 113 117 126 143 144 145 150 160 179 190 196 244 250 259 277 303 331 379 422 433 436 454 463 476 477 480 482 493 503 512 514 517 518 541 542 543 572 584 601 622 634 636 648 687 696 704 706 708 709 711 712 715 717 732 736 750 785 801 813 819 833 848 941 948 950 958 966 1005 1010 1012 1021 1032 1041 1046 1066 1069 1073 1095 1100 1101 1104 1106 1119 1137 1146 1153 1154 1156 1158 1159 1168 1169 1171 1173 1186 1196 1220 1226 1232 1233 1238 1265 1272;
	Charset Bin7 =  7 71 87 90 100 124 139 142 151 155 168 178 193 195 203 204 213 216 226 247 288 289 294 295 306 314 318 319 343 344 354 386 432 442 472 479 488 511 513 522 527 531 533 555 557 560 567 576 579 583 586 589 629 662 676 689 702 703 707 731 737 738 757 824 835 860 862 875 878 935 937 962 991 1000 1002 1003 1006 1044 1048 1065 1072 1074 1093 1218 1223 1225 1242;
	Charset Bin8 =  79 91 94 104 128 131 149 158 186 270 279 280 291 301 302 327 328 329 335 336 337 349 357 377 391 416 458 468 471 489 516 519 534 548 550 585 599 604 609 612 614 628 649 686 690 811 827 830 832 870 879 934 938 972 998 999 1009 1016 1034 1056 1064 1075 1076 1085 1094 1115 1126 1138 1213 1217 1247 1267;
	Charset Bin9 =  8 30 43 48 84 89 95 106 114 127 133 134 136 174 188 217 227 230 243 246 269 351 352 353 359 372 375 381 420 424 431 440 456 457 460 470 473 474 478 492 504 507 509 515 523 524 525 535 537 559 562 587 596 600 611 623 624 627 640 641 650 658 685 713 716 719 721 758 765 851 861 894 901 939 960 970 975 1004 1047 1059 1062 1067 1070 1110 1112 1113 1123 1128 1129 1131 1219 1227 1230 1231 1241 1271;
	Charset Bin10 =  47 49 57 88 105 115 116 132 135 281 300 317 322 345 350 371 373 374 380 421 438 467 469 484 508 510 526 528 536 538 540 546 547 549 613 615 616 621 625 626 700 701 710 714 718 739 740 766 940 959 985 1018 1026 1045 1049 1054 1058 1080 1087 1088 1092 1096 1097 1099 1165 1224 1228 1229 1234;
END;
[START TIME: 16 : 50 : 33 ]
[FINISH TIME: 16 : 50 : 33 ]

注释

Bin数字越大,这个位点演化位点就越大,后面的dataset总结出了根据bin不同而得到的不同位点。但是这个软件是无法删除这些位点的。

引用

Zhang G. Use TIGER to recognize the rapidly evolving sites. malacology.net [Access Time]

Last updated on 6 Dec 2020
Published on 6 Dec 2020

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