current muscle (5) is not compatible

[peterthorpe5]

Dear IImog,

Thank you for the tool - Love it!! Just a heads up the current version of bcgTree does not play well with muscle (5) - current version . The error is:

..../bin/muscle -in gene_tree_120_conserved/TIGR00061.fa -out gene_tree_120_conserved/TIGR00061.aln

Invalid command line
Unknown option in

[09-07 11:29:47] [bcgTree]
[09-07 11:29:47] [bcgTree] ERROR: muscle on TIGR00061 failed

Solution: Downgrade to muscle 3.8

Pete

[iimog]

Hi Pete,
thanks a lot for raising this issue. I'll try to find a way to make bcgTree compatible with old and new versions of muscle. But for now I leave this issue open as information to other users.
Best,
Markus

[iimog]

Making bcgTree work with muscle 5 might be as easy as changing in to align in this line:

bcgTree/lib/bcgTree.pm

Line 224 in dceaf22

my $cmd = $self->{'muscle-bin'}." -in $out/$gene.fa -out $out/$gene.aln";

This would break compatibility with older muscle versions, though. I also need to do some testing that there are no other relevant changes between muscle versions, e.g. in the output format.

[peterthorpe5]

It would break backwards compatibility. Can you extract the version for the -v and apply the command accordingly?

[chiras]

Thanks for raising this, and yes it should be addressed. Thanks @iimog for taking care.

Once this is done, please also update the README, I have a while back made there a comment that only 3.8 is supported for now and posted a link to that binary:

dceaf223a92679e399aab367ca3ef29f618d94b7