Use Blast for the three species of Leishmania in order to take only the common sequences in fasta file

Question

[dzisis1986]

I am using Blastp for the three species of Leishmania (Linfantum, Major, Braziliensis) in order to take only the common sequences in fasta file . I created db of Major and Braziliensis in order to have the Linfantum vs both of them and then i want to create a new fasta of linfantum (linfantum.fasta) only with the sequences which are common.

Do you know how to do this with Blastp ?

Do i have to use a specific evalue parameter ?

[GenoMax]

It may be better to do this using CD-HIT.

[Joe]

If you're just interested in finding core orthologs between genomes, you could also try ROARY.