Gblocks #
在将序列放入系统发育的计算软件(e.g.MrBayes, RAxML等)前,应当先对序列进行一定的处理,具体流程是先进行比对(MAFFT),再进行保守区的选择(GBlocks),之后饱和度检验(DAMBE,Tracer),再是最适模型的选择(jModelTest)。
GBlocks的使用 #
下载地址 将exampleout.fas移入Gblocks.exe的根文件夹,注意序列文件的名称不能过长或者含有一些非法符号,不然会闪退。
******************************************************
GBLOCKS 0.91b
SELECTION OF CONSERVED BLOCKS FROM MULTIPLE ALIGNMENTS
FOR THEIR USE IN PHYLOGENETIC ANALYSIS
******************************************************
o. Open File
b. Block Parameters
s. Saving Options
g. (Get Blocks)
q. Quit
Your Choice:
选择o
Please enter a DNA or protein alignment in NBRF/PIR or FASTA format or a paths file.
File Name:
输入exampleout.fas
******************************************************
GBLOCKS 0.91b
SELECTION OF CONSERVED BLOCKS FROM MULTIPLE ALIGNMENTS
FOR THEIR USE IN PHYLOGENETIC ANALYSIS
******************************************************
CURRENT FILE: exampleout.fas
t. Type Of Sequence: Protein
o. Open File
b. Block Parameters
s. Saving Options
g. Get Blocks
q. Quit
Your Choice:
此时可以选择b
更改一些数值
BLOCK PARAMETERS
1. Minimum Number Of Sequences For A Conserved Position: . 21
2. Minimum Number Of Sequences For A Flank Position: ..... 34
3. Maximum Number Of Contiguous Nonconserved Positions: .. 8
4. Minimum Length Of A Block: ............................ 10
5. Allowed Gap Positions: ................................ None
r. Restore Defaults
g. Get Blocks
z. Extended Block Options
m. Go To Main Menu
Your Choice:
输入对应选项可以修改,也可以不修改,此处不修改,直接选择g
exampleout.fas
Original alignment: 1085 positions
Gblocks alignment: 81 positions (7 %) in 4 selected block(s)
此时根目录里exampleout.fas-gb.htm
是保守区选择信息,将exampleout.fas-gb
修改为exampleoutgb.fas
或者其它以fas
结尾的文件,得到了选择了保守区的序列。