REALPHY specifications

Unique identifier:
OMICS_04245
Software type:
Package/Module, Pipeline/Workflow
Restrictions to use:
None
Programming languages:
Java
Version:
1.12
Requirements:
Bowtie
Maintained:
Yes
Name:
Reference sequence Alignment-based Phylogeny builder
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://realphy.unibas.ch/downloads/RealPhy_v112_source.zip

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REALPHY distribution

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REALPHY specifications

Unique identifier:
OMICS_04245
Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTA, Genbank format
Output format:
FASTA, PHYLIP
Version:
1.12
Maintained:
Yes
Name:
Reference sequence Alignment-based Phylogeny builder
Interface:
Web user interface
Input data:
Raw short-sequence read data sets.
Output data:
An aligned set of orthologous sites (SNPs as well as nonpolymorphic sites), a tree file in Newick format, and multiple tab-delimited files (one for each query genome) containing the positions on the reference genome to which the identified SNPs were aligned.
Computer skills:
Basic
Stability:
Stable

REALPHY support

Documentation

Maintainer

  • Frederic Bertels <>
  • Frederic Bertels <>

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Credits

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Publications

Institution(s)

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland; New Zealand Institute for Advanced Study and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University at Albany, Auckland, New Zealand; Max Planck Institute for Evolutionary Biology, Plon, Germany

Funding source(s)

Supported by the Royal Society of New Zealand with a James Cook Research Fellowship; and the Swiss National Science Foundation with an Ambizione Fellowship (grant number PZ00P3-144605), and a Swiss National Science Foundation Grant (grant number 31003A_135397).

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