OrthoFinder安装及使用

OrthoFinder，主要应用于基因家族分析。

使用OrthoFinder关注的基本生物学问题如下：

Performing a comparative analysis across a clade of species
Identifying orthologs between a pair, or among a small number, of species
Investigating changes at a particular point in evolutionary history

相关教程链接
https://davidemms.github.io/menu/tutorials.html
https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf

一、安装

conda create -n orthofinder
conda activate orthofinder
conda install - c bioconda orthofinder

二、使用

#测试数据一（从github上clone下载整个包，其中包含很多后续会用到的脚本工具）,拷贝ExampleData到virus_orthofinder_analysis文件夹

orthofinder -f ~/input/virus_orthofinder_analysis/

#测试数据二(从Ensembl下载基因组注释pep数据)

wget *
gunzip *.gz
for f in *fa ; do python ~/OrthoFinder/tools/primary_transcript.py $f ; done
orthofinder -f primary_transcripts/

#成功运行会产生如下结果

Results:
    /home/liuxin/input/proteomes/primary_transcripts/OrthoFinder/Results_Nov26/

CITATION:
 When publishing work that uses OrthoFinder please cite:
 Emms D.M. & Kelly S. (2019), Genome Biology 20:238

 If you use the species tree in your work then please also cite:
 Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278
 Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914

三、查看结果

其中(most useful)信息如下：

Comparative_Genomics_Statistics/Statistics_Overall.tsv
Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv
Gene_Duplication_Events/Duplication
Single_Copy_Orthologue_Sequences