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OrthoSelect specifications

Information


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
Requirements
BioPerl, BLAST, ESTScan, GeneWise, Clustalw, Muscle, T-Coffee, HMMER, Gblocks, Aliscore, Noisy
Maintained Yes

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Versioning


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Documentation


Maintainers


  • 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

 (6)
library_books

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

2014
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 […]

call_split

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

2012
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 (). […]

library_books

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

2012
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 […]

library_books

Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

2012
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 […]

library_books

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

2010
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 […]

library_books

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

2009
Nucleic Acids Res
PMCID: 2703962
PMID: 19491309
DOI: 10.1093/nar/gkp434

[…] signed to an OG. This way, the user can easily select OGs with all or a certain percentage of taxa present. Figure 2.Besides an overview of all OGs with sequences assigned (‘All orthologous groups’), OrthoSelect automatically builds a subset of OGs (‘Best orthologous groups’) that have either at least three different taxa or the pre-defined taxa present. The ‘all orthologous groups’ contain all or […]

Citations

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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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