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