I've released version 3.4 of bali-phy. It fixes some bugs, and also
adds 16-state substitution models for RNA stems. You can also select
characters sets from files instead of splitting the files into multiple
The list of changes is available here: http://bali-phy.org/releases/3/
Packages are available for homebrew, Debian, and Ubuntu "Disco Dingo",
or you can download an archive directly at http://bali-phy.org/download.php
P.S. I'm curious if anyone has opinions on how the help looks under
`bali-phy help` and `bali-phy help advanced`.