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:

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

Download


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
dummy: to convert NHX formatted trees to phyloXML
i1:    transfer/split name to taxonomy uniprot identifier (split at underscore if "id_name" pattern, e.g. "817_SusD")
i2:    transfer/split name to taxonomy uniprot identifier (split at underscore if "name_id" pattern, e.g. "SusD_817")


options:
-i       : internal node names in NH or NHX tree are confidence values
-c=<conf>: confidence type (e.g. "bootstrap", default is "unknown")
-ru      : replace all underscores with spaces
-m       : midpoint reroot
-o       : order subtrees
-xt      : extract taxonomy to taxonomy code from "seqname_TAXON"-style names (cannot be used with the following field options: tc, cn, sn)
-xp      : extract taxonomy to taxonomy code from Pfam ("seqname_TAXON/x-y") style names only (cannot be used with the following field options: tc, cn, sn)
-ni      : no tree level indentation in phyloXML output
-iqs     : ignore quotes and whitespace (e.g. "a b" becomes ab)