Garli user guide

A short guide on how to use garli on UPPMAX systems.

GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic
searches on aligned sequence datasets using the maximum-likelihood criterion.

Garli version 2.1 is installed on UPPMAX, both the serial and the parallel (using MPI).

Manual for v.0.96

Serial version

In order to use garli you should first load the garli module

module load garli

Then you can run the serial version of garli with the input specified in the file garli.conf. Copy the Example directory from $GARLI_ROOT  to your home or project folder:

cp -r $GARLI_ROOT/Example <path/of/your/choice>

In Example/basic you will find the garli.conf file plus some examples.

Run with "Garli".

Garli

Here is an example of a job file for the serial version of garli for SLURM:

#!/bin/bash
#SBATCH -J garli-test
#SBATCH -A your_project_name
#SBATCH -p core -n 1
#SBATCH -t 01:00:00
 
module load garli
 
Garli

More information about using Garli may be found on the  Garli homepage.