Hi! I am using Phylophlan 3.0.3. There seems to be a compatibility issue with the way the phylophlan_write_config script creates the muscle command if version 5 is used.
Phylophlan always crashed when using the default command from the automatically generated config:
[msa]
program_name = ~/miniconda3/envs/phylophlan/bin/muscle
params = -quiet -maxiters 2
input = -in
output = -out
version = -version
command_line = #program_name# #params# #input# #output#
But the program ran smoothly after I manually edited the config file to this (based on Muscle5 documentation):
[msa]
program_name = ~/miniconda3/envs/phylophlan/bin/muscle
params = -threads 1
input = -super5
output = -output
version = -version
command_line = #program_name# #input# #output# #params#
If earlier versions of muscle are used this shouldn’t be an issue, but since this is the muscle version that was automatically installed along with phylophlan it should probably be updated