fasttree

Module Name

fasttree

Last Updated On

08/29/2023

Support Level

Primary Support

Software Access Level

Open Access

Home Page

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.

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 small,large,ram256g,ram1t
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

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

Default

2.1.8

Other Modules

2.1.4, 2.1.8

Default

2.1.8

Other Modules

2.1.4, 2.1.8

Default

2.1.8

Other Modules

2.1.4, 2.1.8