Ortholog-Finder statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Ortholog-Finder
info

Tool usage distribution map

This map represents all the scientific publications referring to Ortholog-Finder per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Gene orthology prediction chevron_right
Want to access the full stats & trends on this tool?

Protocols

Ortholog-Finder specifications

Information


Unique identifier OMICS_23371
Name Ortholog-Finder
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A GenBank file or an amino acid sequences file.
Input format GenBank,FASTA
Output data A multi-FASTA format, which includes sequence data of each ortholog or a multi-FASTA-like format that includes all ortholog sequence data in one file.
Output format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 4.07
Stability Stable
Requirements
BLAST+, FastTree, MAFFT, Gblocks, Bioperl, EMBOSS, mcl, OrthoMCL, Java Runtime Environment
Maintained Yes

Download


download.png

Versioning


No version available

Maintainer


  • person_outline Tokumasa Horiike

Publication for Ortholog-Finder

Ortholog-Finder citations

 (4)
library_books

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

2017
Front Genet
PMCID: 5674930
PMID: 29163633
DOI: 10.3389/fgene.2017.00165

[…] the accuracy of the results. It is now at its 1.1.10 version (updated in September 2017) and it depends on the following packages: Python, BLAST+, MCL graph clustering algorithm, MAFFT, and FastTree.Ortholog-Finder is a tool developed to build ortholog data sets for phylogenetic analysis. Results published by its developers suggest that it can tolerate gene loss after gene duplication and HGT, be […]

library_books

The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species

2017
Front Microbiol
PMCID: 5313534
PMID: 28261177
DOI: 10.3389/fmicb.2017.00218

[…] rs (at least two are required) is selected as the best synteny ortholog. The whole workflow is depicted in Figure .The script is available for download at https://github.com/danielwuethrich87/Synteny_ortholog_finder.git. […]

call_split

Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica

2013
BMC Genomics
PMCID: 3866579
PMID: 24341635
DOI: 10.1186/1471-2164-14-885
call_split See protocol

[…] search.php?method=Org_Ppersica). The bioinformatics tools included BLAST searches, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), EuKaryotic Orthologous Groups Database (KOG) and ortholog finder. Arabidopsis sequences were identified using The Arabidopsis Information Resource (TAIR). Amino acid sequences were aligned using ClustalW followed by manual adjustments when needed [] […]

library_books

ECgene: genome annotation for alternative splicing

2004
Nucleic Acids Res
PMCID: 540072
PMID: 15608289
DOI: 10.1093/nar/gki118

[…] ECgene is an ongoing project. It aims to be one of the reference sites for genome annotation. A number of new features and applications are currently under development. Gene profiler, ortholog finder and ChimerDB are among the applications to be completed in the near future. We plan to expand and optimize the system resources to shorten the response time. Other model organisms will […]


Want to access the full list of citations?
Ortholog-Finder institution(s)
Department of Biological and Environmental Science, Shizuoka University, Japan; The Genome Institute, Japanese Foundation of Cancer Research, Tokyo, Japan; Department of Economics, Chiba University of Commerce, Ichikawa, Japan; Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, Kanagawa, Japan; School of New Sciences, Daegu Gyoungbook Institute of Science and Technology, Daegu, Korea
Ortholog-Finder funding source(s)
Supported by the Japan Society for the Promotion of Science, Grant Number 22710184.

Ortholog-Finder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Ortholog-Finder