OrthologID protocols

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OrthologID specifications

Information


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 in pipelines

 (4)
2016
PMCID: 4824122
PMID: 26951781
DOI: 10.1093/gbe/evw043

[…] 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 […]

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 […]

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

[…] d. suzukii scaffolds and d. melanogaster chromosomes were examined using symap version 4.0 () with a minimum size of 500 kb., gene orthology was evaluated using prereleased version 2.0 of the orthologid pipeline. similar to the original version (), the latest version of orthologid takes complete gene sets from all ingroup and outgroup taxa as input and assigns them into gene clusters. […]

2011
PMCID: 3223239
PMID: 22132238
DOI: 10.1371/journal.pone.0028192

[…] the results section for further discussion., among the 2,220 r. parasitica contigs, genemark predicted 2,916 genes for a total of 1,785,377 basepairs. the g+c content pertaining to these was 62.78%. orthologid identified a total of 9,135 orthologous genes among the 51 (including r. parasitica) genomes, 358 of which included an r. parasitica orthologue (3.9% of the total gene-groups). that is, […]


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OrthologID in publications

 (9)
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 […]

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 […]

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 […]

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 […]

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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