MalacoWiki

wiki of malacology

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。

Last updated on 1 Dec 2020
Published on 1 Dec 2020

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