New features include
- Allow multiple separate genes as input
- Each gene may have a different substitution model or indel model
- Decrease the amount of RAM used.
- Speed up the analysis for many taxa (e.g. > 30)
You can download binaries for Linux, Mac, and Windows here:
You can read the updated manual here:
If you have any trouble using bali-phy, let me know. You may want to
join bali-ph...@googlegroups.com if you have not already, and post
your question there.