REALPHY specifications

Information


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

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Documentation


Maintainer


  • person_outline Frederic Bertels <>

Information


Unique identifier OMICS_04245
Name REALPHY
Alternative name Reference sequence Alignment-based Phylogeny builder
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input data Raw short-sequence read data sets.
Input format FASTA, Genbank format
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.
Output format FASTA, PHYLIP
Computer skills Basic
Version 1.12
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Frederic Bertels <>

Publication for Reference sequence Alignment-based Phylogeny builder

REALPHY 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
REALPHY 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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