Software

Treecon-Tools

TREECON-TOOLS

version: 0.1.20060515
contact: jan.wuyts at psb.ugent.be
homepage: http://bioinformatics.psb.ugent.be/software

Description:
This package contains 3 small programs to convert phylogenetic trees between NH or NHX (http://www.genetics.wustl.edu/eddy/forester/NHX.html) and Treecon (http://bioinformatics.psb.ugent.be/psb/Userman/treecon_userman.html) format.

Prerequisites:
These 3 programs are implemented as TCL (http://www.tcl.tk/) scripts. TCL is installed by default on most Unix systems (Linux, MacOS X, Solaris,...). Windows users will first need to install TCL.

Usage:
Extract this tar archive to any directory (for example to your home directory):
tar xvzf treecon_tools.tar.gz

Start the programs with the '-h' switch to read the help information:

$ ~/treecon_tools/nhx2treecon.tcl -h

nhx2treecon.tcl: convert nh or nhx tree file to treecon for windows format default is to accept tree from stdin and write treeconfile to stdout

        Options:
        -i  : use  as Input
        -o  : use  as Output
        -b : use internal node numbers as Bootstrap values
        -n : igNore bootstrap values even if they are present in the nhx
tree
        -d  : reset all Distances to 
(usefull if no distances are given in input tree)
        -s  : Scale all distances by factor .
        -l  (0 < float < 1) : sLide root: distribute
distance from root to outgroup between the 2 horizontal branches.

Since a picture (even if it is ASCII junk) is worth a thousand words, you can use the -l option to convert the tree on the left to the one on the right:

                      *--- org 1                         *--- org 1
                *-----|                            *-----|
                |     *----- org 2                 |     *----- org 2
    *-----------|                              *---|
    |           |     *------ org 3            |   |     *------ org 3
    |           *-----|                        |   *-----|
    |                 *-- org 4                |         *-- org 4
    |                                          |
    *----------- root                          *------------------- root

$ ~/treecon_tools/treecon2nh.tcl -h treecon2nh.tcl: convert treecon tree file to nh file format default is to accept treecon file from stdin and write nh to stdout

        Options:
        -d : Give some more info. Might be usefull for debugging.
        -b : Use bootstrap values as node numbers
        -i  : use  as Input
        -o  : use  as Output

$ ~/treecon_tools/treecon2nhx.tcl -h treecon2nhx.tcl: convert treecon tree file to NHX file format default is to accept treecon file from stdin and write NHX to stdout

        Options:
        -i  : use  as Input
        -o  : use  as Output

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