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OrthoFinder how to find homologous genes, in response to this problem, this article details the corresponding analysis and solutions, hoping to help more small partners who want to solve this problem find a simpler and easier way.

The search for homologous genes is essential for constructing phylogenetic trees of species, calculating kaks, or other analyses of comparative genomics and evolution.

Orthomcl has been introduced before, and Orthomcl is currently the best tool for finding homologous genes, but Orthomcl is cumbersome to use and not fast enough.

OrthoFinder's work flow is shown below

OrthoFinder compares results with other tools as shown below

（Quest for Orthologs benchmarks and Pareto frontier for methods）

As can be seen from the figure, OrthoFinder has a great improvement in speed and accuracy compared to other tools. After OrthoFinder runs, it not only finds homologous genes, but also constructs gene trees and species trees.

A big reason OrthoFinder runs fast is the use of DIAMOND/MMseqs for protein alignment. DIAMOND, in particular, can get results that are basically the same as blast, while running 500x-20, 000x faster than blast.

Install and Run OrthoFinder

1. download and install

https://github.com/davidemms/OrthoFinder

You can download the source code and install it later, or you can install it with conda:

conda install -y orthofinder

PS: Strongly recommend installing DIAMOND

2. Ready to input data

The input data required by OrthoFinder is simple: put the protein sequences of each species into separate fasta files, and then put those fasta files into a directory. The fasta file is named for the corresponding species name.

3. run

orthofinder -f Dataset_ directory

If you want to change the number of threads, use the-t parameter. The default matching tool is DIAMOND, but you can also specify other tools such as blast with-S. Details of other parameters can be seen by running orthofinder -h.

4. outcome document

In the results folder, the Orthogroups folder contains all the homologous gene information, and the single-copy homologous gene information is also thoughtfully given separately. The Gene_Trees and Species_Tree folders are trees constructed of individual homologous genes, respectively, and species trees constructed of all homologous genes have been integrated.

Note:

1. The-M parameter can be specified to specify the algorithm for constructing the species tree. OrthoFinder's default method is the STAG algorithm. STAG integrates all homologous genes (including multi-copy genes), which is especially suitable for species with long genetic distance and few or no single-copy homologous genes.

Similarly, you can specify that only single-copy genes are used to build trees, and-M raxml calls Raxml to build.

2. Orthogroups.GeneCount.tsv in the Orthogroups folder counts the number of homologous genes in each species, which can be used to easily select the genes we need.

About OrthoFinder how to find homologous gene questions to share here, I hope the above content can be of some help to everyone, if you still have a lot of doubts not solved, you can pay attention to the industry information channel to learn more related knowledge.

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