Minnesota Supercomputing Institute
2.1.8
2.1.4, 2.1.8
Monday, July 24, 2017
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.
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
FastTree -gtr -nt alignment_file > tree_file
More documentation can be found here
#!/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