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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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 in publications

 (2)
PMCID: 3444750
PMID: 22993690
DOI: 10.1038/srep00665

[…] 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 […]

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

[…] 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; […]


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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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