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OrthoFinder is a command-line
OrthoFinder is a command-line software tool
A programming tool or software development tool is a computer program that software developers use to create, debug, maintain, or otherwise support other programs and applications. The term usually refers to relatively simple programs, that can b ...
for comparative genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural lan ...
. OrthoFinder determines the correspondence between genes in different organisms (also known as orthology analysis). This correspondence provides a framework for understanding the evolution of life on Earth, and enables the extrapolation and transfer of biological knowledge between organisms.
OrthoFinder takes FASTA files of protein sequences as input (one per species) and as output provides:
* Orthogroups
* Rooted Phylogenetic trees of all orthogroups
* A rooted species tree for the set of species included in the input dataset
* Hierarchical orthogroups for each node in the species tree
* Orthologs between all species
* Gene duplication
Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. ...
events mapped to branches in the species tree
* Comparative genomic statistics
As of August 2021, the tool has been referenced by more than 1500 published studies.{{cite web, url=https://scholar.google.co.nz/scholar?cites=10931031451104788868&as_sdt=2005&sciodt=0,5&hl=en, website=Google Scholar, title=Citations for Emms & Kelly 2015, access-date=6 August 2021
See also
*Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
* Homology (biology)
In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of pri ...
* Sequence homology
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spe ...
* Protein family
A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be c ...
* Sequence clustering In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" ( ESTs) or protein origin.
For proteins, homologous sequences are typicall ...
References