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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
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.
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:
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
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