OrthoFinder

https://www.jianshu.com/p/3d0051edde97?utm_campaign=haruki&utm_content=note&utm_medium=seo_notes&utm_source=recommendation
https://www.jianshu.com/p/16e0bbb2ba19

1. 将需要进行比对物种(2个或者以上)的蛋白质fasta数据放在同一个目录下

(base) zhiyong@zhiyong-OptiPlex-7050:~/Desktop/kkk/kkkk$ ll
总用量 35864

drwxrwxr-x 3 zhiyong zhiyong     4096 8月   3 20:14 ./
drwxrwxr-x 3 zhiyong zhiyong     4096 8月   3 20:14 ../
-rw-rw-r-- 1 zhiyong zhiyong 15606298 12月 18  2019 GCF_001442555.1_ACSNU-2.0_protein.faa
-rw-rw-r-- 1 zhiyong zhiyong 21100234 8月   8  2019 GCF_003254395.2_Amel_HAv3.1_protein.faa

2. 进行比对

orthofinder -f path-to-fasta -S method-to-align

• 1. -f: 指定蛋白质fasta文件放置的路径
• 2. -S: 指定用于比对的方式，包括blast, mmseqs, blast_gz和diamond

3. 结果

3.1 比对结果统计文件

Orthogroups/Orthogroups.GeneCount.tsv

Orthogroup  GCF_001442555.1_ACSNU-2.0_protein   GCF_003254395.2_Amel_HAv3.1_protein Total
OG0000000   1   50  51
OG0000001   5   42  47
OG0000002   0   46  46
OG0000003   1   43  44
OG0000004   1   37  38
OG0000005   0   38  38
OG0000006   0   36  36
OG0000007   1   34  35
OG0000008   0   33  33

可以根据以上的统计结果来选择1-to-1的同源基因

3.2 1-to-1同源基因

Orthogroups/Orthogroups_SingleCopyOrthologues.txt

这个文件中给出了所有1-to-1同源基因所在的orthologous group

3.3 各个orthologous group所包含的各个物种的translation-ID

(base) zhiyong@zhiyong-OptiPlex-7050:~/Desktop/kkk/kkkk/OrthoFinder/Results_Aug03/Orthogroups$ cat Orthogroups.tsv|head -2
Orthogroup  GCF_001442555.1_ACSNU-2.0_protein   GCF_003254395.2_Amel_HAv3.1_protein
OG0000000   XP_028519937.1  XP_026294641.1, XP_026294642.1, XP_026294643.1, XP_026294644.1, XP_026294645.1, XP_026294646.1, XP_026294647.1, XP_026294648.1, XP_026294649.1, XP_026294650.1, XP_026294651.1, XP_026294652.1, XP_026294653.1, XP_026294654.1, XP_026294655.1, XP_026294656.1, XP_026294657.1, XP_026294658.1, XP_026294659.1, XP_026294660.1, XP_026294661.1, XP_026294662.1, XP_026294663.1, XP_026294664.1, XP_026294665.1, XP_026294666.1, XP_026294667.1, XP_026294668.1, XP_026294669.1, XP_026294670.1, XP_026294671.1, XP_026294672.1, XP_026294673.1, XP_026294674.1, XP_026294675.1, XP_026294676.1, XP_026294677.1, XP_026294678.1, XP_026294679.1, XP_026294680.1, XP_026294681.1, XP_026294682.1, XP_026294683.1, XP_026294684.1, XP_026294685.1, XP_026294686.1, XP_026294687.1, XP_026294688.1, XP_026294689.1, XP_026294690.1