phyloxml converter

Overview

phyloxml_converter is a simple Java command line tool to convert various phylogentic tree formats to phyloXML ("newick to phyloxml").
It can read trees in the following formats:

New Hampshire/Newick — produced by most major phylogenetic analysis software (e.g. PHYLIP)
NHX — New Hampshire Extended (deprecated) — our extension of the New Hampshire format
Nexus — the format used by PAUP*, MrBayes, and many others
ToL Response XML Format — the format currently used by the Tree of Life project webservices

It is implemented in Java as part of the forester libraries.
A similar, but more flexible, tool is the phylogeny decorator: decorator

Download

» forester.jar

Source code is available at [forester] at sourceforge.net

Usage

java -cp path\to\forester.jar org.forester.application.phyloxml_converter -f=<field option> [options] <infile> <outfile> field options: nn: transfer name to node/clade name tc: transfer name to taxonomy code sn: transfer name to taxonomy scientific name cn: transfer name to taxonomy common name gn: transfer name to sequence name sy: transfer name to sequence symbol options: -i : internal names in NH or NHX tree are bootstrap support values -ru: replace all under scores with spaces -qs: allow quotation marks and spaces (default: ignore) -m : midpoint reroot -o : order subtrees -ni: no tree level indendation in phyloXML output

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Contact

Christian M Zmasek
Burnham Institute for Medical Research | cmzmasek yahoo com

Last updated 2009.07.10