Usage

Configuration File

Phyluce is looking for the config file in a couple of default locations one of which is ~/.phyluce.conf. We provide a basic working configuration file at $HPC_PHYLUCE_CONF/phyluce.conf, which should be used automatically by phyluce executables. However, if you need to change the parameters you can copy it to your home directory with:

$ ml phyluce
$ cp $HPC_PHYLUCE_CONF/phyluce.conf ~/.phyluce.conf

See Phyluce Documentation about using your personal copy of phyluce.conf to make any changes you need.

UF Research Computing added a custom environment variable for Phyluce for researchers who need to provide custom MAFFT arguments. Export the PHYLUCE_MAFFT_ARGS environment variable with the arguments e.g.

export PHYLUCE_MAFFT_ARGS="--reorder --adjustdirectionaccurately --anysymbol --maxiterate 1000 --retree 1 --genafpair"