Hi Cedric,
I checked that this command works on the binaries of 4.0-beta2 released
on github.
Did you by chance compile from source in the last few days? If so, then
you've probably included some changes towards 4.0-beta3 that are not
released yet. I've changed the version number to 4.0-beta3-preview and
modified the NEWS file to reflect this.
The simplest thing might be to just replace '+' with '+>':
bali-phy OG6_100154.fasta --package-path /scratch/chauvec/bali-phy/lib/bali-phy/ -S 'tn93+>Rates.gamma+>inv'
You will also need to put the substitution model in quotes, since the
shell will otherwise eat the '>' character. Alternatively, you could
run 'git checkout 4.0-beta2' to go back to 4.0-beta2, which still allows
the old syntax.
BTW, usually it is not necessary to specify the package path, since
bali-phy can figure it out relative to the location of the bali-phy
executable. Is that not working for you?
-BenRI