1.介绍
OrthoFinder用于鉴定直系同源基因群(orthogroups)、推断基因树和物种树，在此基础上推断基因复制事件并生成大量的统计文件。
2.安装
conda create -n orthofinder3 python=3.10
conda activate orthofinder3
conda install orthofinder
3.使用
3.1 基础知识
3.2 帮助命令
$ orthofinder --help
SIMPLE USAGE:
Run full OrthoFinder analysis on FASTA format proteomes in <dir>
orthofinder [options] -f <dir>
To assign species from <dir1> to existing OrthoFinder orthogroups in <dir2>
orthofinder [options] --assign <dir1> --core <dir2>
OPTIONS:
-t <int> Number of parallel sequence search threads [Default = 48]
-a <int> Number of parallel analysis threads
-M <txt> Method for gene tree inference. Options "dendroblast" & "msa" [Default = msa]
-S <txt> Sequence search program [Default = diamond]
Options: diamond, diamond_ultra_sens, blastp, mmseqs, blastn
-A <txt> MSA program, requires "-M msa" [Default = famsa]
Options: muscle, mafft, famsa
-T <txt> Tree inference method, requires "-M msa" [Default = FastTree]
Options: fasttree, fasttree_fastest, raxml, iqtree3
-s <file> User-specified rooted species tree
-I <int> MCL inflation parameter [Default = 1.2]
-n <txt> Name to append to the results directory
-o <txt> Non-default results directory
-d Input is DNA sequences.
-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)
-h Print this help text
WORKFLOW STOPPING OPTIONS:
-op Stop after preparing input files for BLAST
WORKFLOW RESTART COMMANDS:
-b <dir> Start OrthoFinder from pre-computed BLAST results in <dir>
VERSION:
-v Show the current version number
LICENSE:
Distributed under the GNU General Public License (GPLv3). See License.md
CITATION:
When publishing work that uses OrthoFinder please cite:
Emms D.M., Liu Y., Belcher L., Holmes J. & Kelly S. (2025), bioRxiv
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
