README
FILE FOR TCS
TCS
version 1.09
The
input format for the TCS (Templeton et al, 1992) program is a DNA alignment in
NEXUS SEQUENTIAL (example.nex) or PHYLIP SEQUENTIAL(example.phy). The program will collapse sequences into
haplotypes and proceed to the cladogram estimation. It will save a graph
(dataname.graph) that you can open later.
You can
specify whether you want to treat gaps as a 5th state or as missing data.
You can
select, create and delete nodes o branches on the graph. You can use several
algorithms to reorganize the graph. You can move them around and save the file
as postcript.
We
included an option to read a matrix of absolute distances AMONG HAPLOTYPES. The
matrix should be LOWER DIAGONAL in NEXUS (example_dis.nex) or PHYLIP (example_dis.phy)
format.
IMPORTANT:
you have to add the "nchar" to these files, so the 95% connection
limit can be calculated. Look a the example files.
We will
add new features to the next versions and try to correct potential bugs. If you
are using this program, we should know that, so we can inform you about
mistakes and new versions.
BUGS;
Fixed
in version 1.06
When collapsing sequences to haplotypes, the
program was making some mistakes in some cases when the missing gaps options
was ON.
Fixed
in version 1.09
Fixed
bug that was creating several unconnected haplotyped (when they should be
connected) for some big data sets.
PICT
files
The
PICT files that the programs outputs work fine in the Windows version. In the
Macintosh version they are not ready.
February
2001
David
Posada
david.posada@.byu.edu