OrthoFinder

Overview

OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.

Using

Use the module name orthofinder to discover versions available and to load the application.

Example

[]$ orthofinder --help OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms SIMPLE USAGE: Run full OrthoFinder analysis on FASTA format proteomes in <dir> orthofinder [options] -f <dir> Add new species in <dir1> to previous run in <dir2> and run new analysis orthofinder [options] -f <dir1> -b <dir2> OPTIONS: -t <int> Number of parallel sequence search threads [Default = 4] -a <int> Number of parallel analysis threads -d Input is DNA sequences -M <txt> Method for gene tree inference. Options 'dendroblast' & 'msa' [Default = dendroblast] -S <txt> Sequence search program [Default = diamond] Options: blast, diamond, diamond_ultra_sens, blast_gz, mmseqs, blast_nucl -A <txt> MSA program, requires '-M msa' [Default = mafft] Options: mafft, muscle -T <txt> Tree inference method, requires '-M msa' [Default = fasttree] Options: fasttree, raxml, raxml-ng, iqtree -s <file> User-specified rooted species tree -I <int> MCL inflation parameter [Default = 1.5] -x <file> Info for outputting results in OrthoXML format -p <dir> Write the temporary pickle files to <dir> -1 Only perform one-way sequence search -X Don't add species names to sequence IDs -y Split paralogous clades below root of a HOG into separate HOGs -z Don't trim MSAs (columns>=90% gap, min. alignment length 500) -n <txt> Name to append to the results directory -o <txt> Non-default results directory -h Print this help text WORKFLOW STOPPING OPTIONS: -op Stop after preparing input files for BLAST -og Stop after inferring orthogroups -os Stop after writing sequence files for orthogroups (requires '-M msa') -oa Stop after inferring alignments for orthogroups (requires '-M msa') -ot Stop after inferring gene trees for orthogroups WORKFLOW RESTART COMMANDS: -b <dir> Start OrthoFinder from pre-computed BLAST results in <dir> -fg <dir> Start OrthoFinder from pre-computed orthogroups in <dir> -ft <dir> Start OrthoFinder from pre-computed gene trees in <dir> LICENSE: Distributed under the GNU General Public License (GPLv3). See License.md CITATION: When publishing work that uses OrthoFinder please cite: Emms D.M. & Kelly S. (2019), Genome Biology 20:238 If you use the species tree in your work then please also cite: Emms D.M. & Kelly S. (2017), MBE 34(12): 3267-3278 Emms D.M. & Kelly S. (2018), bioRxiv https://doi.org/10.1101/267914

Using Multiple Cores/Threads

The orthofinder application allows you to define multiple cores/threads within calls using the '-t for number of threads allocated to the program' option.

After downloading the example files, a batch script would take the following form where we are defining and using 8 cores (on a single node).

... #SBATCH --cpus-per-task=8 ... orthofinder -f ./ExampleData -t 8

The best number of cores/threads and memory to use for a particular job will depend on the data and is up to the researcher to explore.

Please feel free to report/share any interesting observations and we can update this page.