msa example?

[KarlFetter]

Hi, can you post an example for using the msa? I’m getting hung up on how to specify the reference sequence. I have the sequence in a file called ref.fa and I’m getting a ERROR: Node ref.fa not found. with this command: coati msa -m mar-ecm -o global_tps global_tps.fa global_tps.tre ref.fa

Thanks!

[reedacartwright]

@KarlFetter Instead of 'ref.fa', try using the name of the sequence in global_tps.fa that you want to use as the reference. Of course, this sequence would need to be in global_tps.fa.