OrthoFinder protocols

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OrthoFinder specifications


Unique identifier OMICS_09733
Name OrthoFinder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of protein sequences, one per species.
Input format FASTA
Output data A set of files describing the orthogroups, orthologs, gene trees, resolve gene trees, the rooted species tree, gene duplication events and comparative genomic statistics for the analyzed species.
Output format TXT+CSV
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.3.1
Stability Stable
Maintained Yes



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  • person_outline Steven Kelly <>
  • person_outline David Emms <>

Additional information


Publications for OrthoFinder

OrthoFinder in pipelines

PMCID: 5698912
PMID: 29188023
DOI: 10.5256/f1000research.13945.r27739

[…] annotations [ p. infestans , p. kernoviae , p. lateralis , p. nicotianae , p. parasitica (p1569_v1; broad institute), p. ramorum , p. sojae and p. cinnamomi var. cinnamomi]. accordingly, we used orthofinder v1.1.10 with default parameter values, except we used diamond as the alignment program with the diamond_more_sensitive flag. orthofinder first identifies ‘orthogroups’ (an extension […]

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

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

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

[…] only the longest isoform per gene), as well as against the phylofish brown trout and european whitefish assemblies (75,388 and 74,701 transcripts respectively) []., second, we used the program orthofinder v1.1.2 [] to identify orthologous groups of proteins amongst our four assemblies using blast all-v-all (self and reciprocal blasts simultaneously) algorithm and to further quantify […]

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 , aligned using t-coffee , concatenated and trimmed using gblocks before the resulting alignment (296,082 amino acids in length) was used to construct a core genome maximum likelihood […]

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OrthoFinder in publications

PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] magnaporthe oryzae, neonectria ditissima, neurospora crassa, sclerotinia sclerotiorum, trichoderma reesei and ustilago maydis, 1032 single copy genes shared by all genomes were selected by orthofinder and aligned with mafft (mafft-linsi-anysymbol) [, ]. the phylogenomic tree was constructed using fasttree based on the alignments of single-copy ortholog families […]

PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] domains that are specific to repetitive elements., to determine relationships between p. andersonii and t. orientalis genes, as well as with other plant species, we inferred orthogroups with orthofinder version 0.4.0 (). as orthogroups are defined as the set of genes that are descended from a single gene in the last common ancestor of all of the species being considered, […]

PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] sequence and these areas largely correspond to hypothetical genes (additional files  & )., to explore differences in gene content between the four genomes, we examined predicted proteins using orthofinder []. using an evidence-based annotation methodology for eukaryotic genomes, we identified 3675, 3624 and 4789 genes in the robertson, fish creek and goon nure strains, compared with 4002 […]

PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] (act) v13.0.0 with a gc window size 1000 bp and alignments filtered by score length of 2000 bp for visualisation., orthologous protein clustering of predicted protein sequences was conducted with orthofinder version 1.1.4 [] at an expected value 0.001. a venn diagram of protein orthologous groups was constructed with jvenn []., gene functional annotation (e.g. go and interpro terms) […]

PMCID: 5952958
DOI: 10.1093/gbe/evy081

[…] per million years, respectively. for the global analysis, we estimated the average values across all branches, excluding li. polyphemus, which was used to root the tree. we used the software orthofinder () to obtain orthogroups (i.e., all groups of n: n orthologs) and gene trees to calculate the number of gene gain and loss events in each lineage with the program notung (). finally, […]

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

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