OrthoFinder pipeline

OrthoFinder specifications


Unique identifier OMICS_09733
Name OrthoFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data OrthoFinder takes as input a directory of FASTA files, one per species.
Output data It outputs a file containing the orthologous groups of genes from these species.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.2.7
Stability Stable
Requirements Scipy, BLAST+, The MCL graph clustering algorithm
Maintained Yes



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  • person_outline Steven Kelly <>

Publication for OrthoFinder

OrthoFinder IN pipelines

PMCID: 5753479
PMID: 29298680
DOI: 10.1186/s12864-017-4382-2

[…] searches the peptides for protein domains against the pfam database (release 30.0) [55], a collection of protein family alignments. these sets of amino acid sequences were further analyzed by the orthofinder pipeline (v1.1.4) [56] to identify orthogroups of the three assemblies, using the poecilia reticulata proteome as reference [57]. afterward, the orthogroups were annotated with goblet […]

PMCID: 5759245
PMID: 29310597
DOI: 10.1186/s12864-017-4379-x

[…] between the published set of atlantic salmon refseq proteins, further validates the completeness and quality of the assemblies presented here. this statement is further supported by the additional orthofinder analyses we performed comparing the orthogroup distribution size of the current salmon assembly (at all four filtering steps: unfiltered, after transdecoder single-best orf prediction, […]

PMCID: 5824068
PMID: 29483968
DOI: 10.7150/jgen.22986

[…] basis of the core proteins conserved among 11 geobacillus and 7 parageobacillus genomes, including the 3 genomes sequenced in this study. a total of 1,355 conserved proteins were identified using orthofinder 15, aligned using t-coffee 16, concatenated and trimmed using gblocks 17 before the resulting alignment (296,082 amino acids in length) was used to construct a core genome maximum […]

PMCID: 5826968
PMID: 29520261
DOI: 10.3389/fmicb.2018.00338

[…] enrichment was calculated by the δδct method (livak and schmittgen, 2001). results shown represent average enrichment for three biological replicates., orthologous groups were identified using orthofinder (emms and kelly, 2015), by which all nucleotide sequences were compared using a blastn all-against-all search with an e-value cutoff of <10-4. nucleotide sequences used to construct […]

PMCID: 5844296
PMID: 29311113
DOI: 10.1534/g3.117.300316

[…] m. guilliermondii (gca_000149425.1 and gca_900174495.1), m. caribbica (gca_000755205.1), c. carpophila (gca_001599235.1), and c. lusitaniae (gca_000003835.1)., orthogroups were inferred with orthofinder 1.1.4 (emms and kelly 2015) from the predicted sets of proteins. single-copy orthogroups (sco) were then selected, defined as orthogroups with exactly one protein in all samples, […]

OrthoFinder institution(s)
Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK

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