OrthoFinder-Teaching
Category
Bioinformatics
Program On
Teaching
Version
2.1.2
Author / Distributor
Description
"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." More details are at OrthoFinder
Running Program
The last version of this application is at /usr/local/apps/gb/orthofinder/2.1.2
To use this version, please load the module with
ml orthofinder/2.1.2
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_OrthoFinder
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=OrthoFinder.%j.out
#SBATCH --error=OrthoFinder.%j.err
cd $SLURM_SUBMIT_DIR
ml orthofinder/2.1.2
orthofinder.py [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml orthofinder/2.1.2
orthofinder.py -h
OrthoFinder version 2.1.2 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 = 16]
-a <int> Number of parallel analysis threads [Default = 1]
-M <txt> Method for gene tree inference. Options 'dendroblast' & 'msa'
[Default = dendroblast]
-S <txt> Sequence search program [Default = blast]
Options: blast, blast_gz, diamond
-A <txt> MSA program, requires '-M msa' [Default = mafft]
Options: mafft, muscle, mafft
-T <txt> Tree inference method, requires '-M msa' [Default = fasttree]
Options: mafft, iqtree, fasttree, raxml
-R <txt> Tree reconciliation method [Default = of_recon]
Options: of_recon, dlcpar, dlcpar_deepsearch
-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
-n <txt> Name to append to the 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. (2015), Genome Biology 16:157
Installation
Source code is obtained from OrthoFinder
System
64-bit Linux