GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion. Several sequence types are supported, including nucleotide, amino acid and codon. Version 2.0 adds support for partitioned models and morphology-like datatypes.
You can run garli on our standalone machines or the cluster.
First create a
garli.conf file in your working directory along with your data file. There are many options in the documentation. Here is an example
garli.conf file to get you started (you will need to alter this to suite your analysis):
[general] datafname = rana.nex constraintfile = none streefname = stepwise attachmentspertaxon = 50 ofprefix = example_output randseed = -1 availablememory = 512 logevery = 10 saveevery = 100 refinestart = 1 outputeachbettertopology = 0 outputcurrentbesttopology = 0 enforcetermconditions = 1 genthreshfortopoterm = 20000 scorethreshforterm = 0.05 significanttopochange = 0.01 outputphyliptree = 0 outputmostlyuselessfiles = 0 writecheckpoints = 0 restart = 0 outgroup = 1 resampleproportion = 1.0 inferinternalstateprobs = 0 outputsitelikelihoods = 0 optimizeinputonly = 0 collapsebranches = 1 searchreps = 2 bootstrapreps = 0 [model1] datatype = nucleotide ratematrix = 6rate statefrequencies = estimate ratehetmodel = gamma numratecats = 4 invariantsites = estimate [master] nindivs = 4 holdover = 1 selectionintensity = 0.5 holdoverpenalty = 0 stopgen = 5000000 stoptime = 5000000 startoptprec = 0.5 minoptprec = 0.01 numberofprecreductions = 10 treerejectionthreshold = 50.0 topoweight = 1.0 modweight = 0.05 brlenweight = 0.2 randnniweight = 0.1 randsprweight = 0.3 limsprweight = 0.6 intervallength = 100 intervalstostore = 5 limsprrange = 6 meanbrlenmuts = 5 gammashapebrlen = 1000 gammashapemodel = 1000 uniqueswapbias = 0.1 distanceswapbias = 1.0
slurm submission script.
#!/bin/sh #PBS -l nodes=5:ppn=4 #PBS -q short #PBS -N GarliTest # Initialize and load the modules . /usr/modules/init/bash module load openmpi-apps/1.6.4/garli/2.01 cd $PBS_O_WORKDIR mpirun -np 20 Garli-2.01
#!/bin/sh #SBATCH -N 5 -c 4 #SBATCH -J GarliTest # Initialize and load the modules . /usr/modules/init/bash module load openmpi-apps/1.10.2/garli/2.01 cd "$SLURM_SUBMIT_DIR" mpirun Garli-2.01 -20
You can optionally specifiy a number of replicates after the
Garli-2.01 command. See the Garli Documentation. Note that the total number of replicates performed also depends on the
searchreplicates parameter in the
Note: at least with recent tests under Slurm, specifying a the number of processes
Garli-2.01 command is necessary. See the Slurm script above.