# fasttree

## Summary

+ **Module Name:** fasttree
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://www.microbesonline.org/fasttree/](http://www.microbesonline.org/fasttree/)

## Software Description

FastTree infers approximately-maximum-likelihood phylogenetic trees from
alignments of nucleotide or protein sequences. FastTree can handle
alignments with up to a million of sequences in a reasonable amount of
time and memory. For large alignments, FastTree is 100-1,000 times
faster than PhyML 3.0 or RAxML 7.
## General Linux

To load this software in a Linux environment run the commands:

    module load fasttree

To infer a tree for a protein alignment with the JTT+CAT model, use

    FastTree < alignment_file > tree_file

or

    FastTree alignment.file > tree_file

To infer a tree for a nucleotide alignment with the GTR+CAT model, use

    FastTree -gtr -nt < alignment.file > tree_file

or

    FastTree -gtr -nt alignment_file > tree_file

More documentation can be found
[here](http://www.microbesonline.org/fasttree/#Usage)
## Slurm Example


	#!/bin/bash
	#SBATCH --job-name="rfm_RunFASTTREETest_job"
	#SBATCH --ntasks=1
	#SBATCH --ntasks-per-node=1
	#SBATCH --output=rfm_RunFASTTREETest_job.out
	#SBATCH --error=rfm_RunFASTTREETest_job.err
	#SBATCH --time=0:10:0
	#SBATCH -p msismall
	module load fasttree/2.1.8
	wget https://public.s3.msi.umn.edu/reframe/sw/fasttree/seq.nast
	fasttree -nt seq.nast > tree
	diff tree ref_tree