How can I run All-v-all BLAST

Question

[Esaie]

Hello, I order to run completely orthoMCL, i must run All-v-all BLAST on my goodProteins.fasta file, but I dont understand very well how to run it by using these paramters -F 'm S' -v 100000 -b 100000 -z protein_database_size -e 1e-5, Can anyone who already done it can help me or give me an commande samples please . Tank you

[GenoMax]

Command line options for blast can be found here and a comprehensive command line blast manual is here.

And this OrthoMCL practical guide.

[Esaie]

Tank you, I am going to read right now.

Answer 1

[ALchEmiXt]

Not sure if you need to stick to running orthoMCL for your question. I have really good experience with proteinortho5 (which is also really fast). Its usages is also very simple.

[ALchEmiXt]

oh my bad. Seems orthoMCL is an ortholog classifier...