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Citations per year

Number of citations per year for the bioinformatics software tool OrthoSelect

Tool usage distribution map

This map represents all the scientific publications referring to OrthoSelect per scientific context
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OrthoSelect specifications


Unique identifier OMICS_24452
Name OrthoSelect
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
BioPerl, BLAST, ESTScan, GeneWise, Clustalw, Muscle, T-Coffee, HMMER, Gblocks, Aliscore, Noisy
Maintained Yes




No version available



  • person_outline Fabian Schreiber
  • person_outline Kerstin Pick
  • person_outline Dirk Erpenbeck
  • person_outline Gert Wörheide
  • person_outline Burkhard Morgenstern

Publications for OrthoSelect

OrthoSelect citations


Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

Mol Biol Evol
PMCID: 4209138
PMID: 25158799
DOI: 10.1093/molbev/msu245

[…] ology inference methods have been applied to phylogenomic analyses based on transcriptomes and low-coverage genomes, such as orthoMCL (), Hcluster_sg (as part of TreeFam; ), SCaFoS (), HaMStR (), and OrthoSelect (). Emerging tools such as OMA-GETHOGs (; ) and Agalma () have also attracted interest in their phylogenomic applications. Among them, HaMStR is by far the most widely used. HaMStR is base […]


Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

Genome Biol Evol
PMCID: 3542558
PMID: 23175716
DOI: 10.1093/gbe/evs104
call_split See protocol

[…] 454 Life Sciences Corporation, Software Release: 2.5.3 [20101207_1124]). For all three new EST-projects, the function of genes was analyzed by KOG (Clusters of eukaryotic orthologous groups) () using OrthoSelect (). […]


Integrating multi origin expression data improves the resolution of deep phylogeny of ray finned fish (Actinopterygii)

Sci Rep
PMCID: 3444750
PMID: 22993690
DOI: 10.1038/srep00665

[…] es, ESTs, mRNAs, Unigenes or cDNAs for 21 other species were downloaded from public databases (see methods). Based on these multi-origin expression data, we obtained 274 orhtologue groups (OGs) using OrthoSelect. The data profile for each species used in this study is shown in . Information for each OG (the number of species, length of alignment, percentage of missing data, best-fitting models of […]


Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

PLoS One
PMCID: 3338709
PMID: 22558409
DOI: 10.1371/journal.pone.0036256

[…] 165 bp in the transcriptome of the African lungfish. On the basis of these multi-origin expressed sequences (transcriptomes, ESTs, mRNAs, and cDNAs), we obtained 4682 ortholog groups with the help of OrthoSelect , . After removing ambiguously aligned blocks and random similarity within multiple sequence alignments, 111 ortholog groups meet our criteria: (a) those found in more than six species; (b […]


Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

BMC Genomics
PMCID: 2867826
PMID: 20361874
DOI: 10.1186/1471-2164-11-222

[…] g paralogues. The C. elegans gene(s) in that group were then classed as orthologues of the parasite EST and our drug target selection criteria were applied to these C. elegans genes. A caveat to this OrthoSelect/OrthoMCL clustering approach is that members of a recently diverged gene family, or some genes that share only a common domain, may be classified here as paralogues, even where they now ha […]


OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences

Nucleic Acids Res
PMCID: 2703962
PMID: 19491309
DOI: 10.1093/nar/gkp434

[…] nces should be used.A reliable protocol is needed to build sets of orthologous sequences from EST libraries for successive phylogenomic analyses. We recently proposed such a protocol, which we called OrthoSelect (Schreiber et al., manuscript submitted). The workflow of the protocol is outlined in . The main idea is to keep user interaction simple, by simultaneously using state-of-the-art methods f […]

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OrthoSelect institution(s)
Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany; Department für Geo- und Umweltwissenschaften, Ludwig-Maximilians-Universität, München, Germany
OrthoSelect funding source(s)
Supported by the German Research Foundation (DFG, Project Wo896/6- 1,2) within DFG Priority Programme SPP 1174 "Deep Metazoan Phylogeny", and by the German Federal Ministry of Research and Education (BMBF) project "MediGRID" (BMBF 01AK803G).

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