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OrthologID specifications

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Unique identifier OMICS_05346
Name OrthologID
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for OrthologID

OrthologID citations

 (10)
call_split

Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk Eyed Flies (Diopsidae)

2016
PMCID: 4824122
PMID: 26951781
DOI: 10.1093/gbe/evw043
call_split See protocol

[…] other insect species (d. melanogaster, d. pseudoobscura, d. virilis, an. gambiae, ae. aegypti, c. quinquefasciatus, bombyx mori and apis mellifera) and assembled into gene family clusters using orthologid (). the proteins from the nondiopsid insects only included the single longest translation for each gene., orthologid uses an markov cluster algorithm (mcl) in which sequences are initially […]

library_books

Extracting phylogenetic signal and accounting for bias in whole genome data sets supports the Ctenophora as sister to remaining Metazoa

2015
PMCID: 4657218
PMID: 26596625
DOI: 10.1186/s12864-015-2146-4

[…] in our dataset. additional file : table s1 lists these species and the genome databases from which they were obtained., gene orthology analysis was performed using a pre-release version 2.0 of the orthologid pipeline []. this version of orthologid uses the mcl algorithm [, ] for improved clustering and includes automated extraction of orthologs from gene trees into a partitioned matrix. amino […]

library_books

Genome of Drosophila suzukii, the Spotted Wing Drosophila

2013
PMCID: 3852387
PMID: 24142924
DOI: 10.1534/g3.113.008185

[…] transcriptomes from the drosophila modencode project (), and then annotated using maker2 () with the same ab initio gene predictors and protein homology–based evidence as our d. suzukii annotation. orthologid then performed sequence alignment using mafft version 7.017b () and parsimony phylogenetic inference using paup* () for each gene cluster and extracted one or more sets of orthologous […]

library_books

Gene family assignment free comparative genomics

2012
PMCID: 3526435
PMID: 23281826
DOI: 10.1186/1471-2105-13-S19-S3

[…] similarity. sometimes such groups are called gene families, thus we will stick to this notion in the following., various databases exist, such as cog [], eggnog [], inparanoid [], treefam [], and orthologid [] (only to name a few) that offer gene family information. these databases can be divided into two groups: databases that primarily use sequence similarity to cluster genes into groups […]

library_books

Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters

2012
PMCID: 3342878
PMID: 22454131
DOI: 10.1093/gbe/evs032

[…] sequence identity, as with cog (), toga (), orthomcl (), mbgd (), toast (), inparanoid (), eggnog (), and orthodb (). the other is to construct phylogenetic trees, as in hogenom (), phyop (), orthologid (), treefam (), loft (), synergy (), phylomedb (), mestortho (), evola (), phog (), ensemblcompara (), and panther ()., these methods usually assign orthologs using genomic content […]

library_books

A Functional Phylogenomic View of the Seed Plants

2011
PMCID: 3240601
PMID: 22194700
DOI: 10.1371/journal.pgen.1002411

[…] underlying darwin's abominable mystery on the sudden appearance and rapid diversification of flowering seed plants, but also on the persistence of the gymnosperms over evolutionary time., we used orthologid (oid) – a program for automated, parsimony tree-based orthology determination, to identify 22,833 sets of orthologs from 150 plant species (see for a description of the extended oid […]


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OrthologID institution(s)
Department of Biology, Montclair State University, Montclair, NJ, USA

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