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FastME

FastME is a distance based phylogeny reconstruction program that works on distance matrices and sequence data.

FastME is available as a module on Apocrita.

Usage

To run the latest installed version of FastME, simply load the fastme module:

$ module load fastme
$ fastme --help

fastme [-i input data file] [-u input user tree file]
[-o output tree file]  [-O output matrix file]  [-I output information file]
[-B output bootstrap trees file] [-a] [-m method] [ -D[model] | -P[model] ]
[-r] [-e] [-g[alpha]] [-n[NNI]] [-s] [-w branch] [-d datasets] [-b replicates]
[-z seed] [-c] [-f] [-T number of threads] [-v] [-V] [-h]

For full usage documentation, run fastme --help.

Core Usage

To ensure that FastME uses the correct number of cores, the -T ${NSLOTS} option should be used.

Example job

Serial job

Here is an example job running on 1 cores and 1GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load fastme

fastme -i input_file.phy \
       -o output_tree_file.tree \
       -T ${NSLOTS}

References