README FILE FOR TCS
TCS version 1.15
Changes to the cladogram will now be reflected when nesting is
performed. The nesting algorithm
uses the most recently saved graph.
Allows the user to specify the % connection limit, or explicitly
define the number of steps to use.
The user is prompted for the file in which to save nesting output.
TCS version 1.13
The input format for the TCS (Templeton et al, 1992) program is a DNA
alignment in NEXUS SEQUENTIAL (example.nex) or
PHYLIPSEQUENTIAL(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
AMONGHAPLOTYPES. 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 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 or NEW FEATURES;
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.
Version 1.12
- Fixed bug that was creating several unconnected haplotyped (when
they should be connected) for some big data sets.
Version 1.13
- Fixed bug that was creating several unconnected haplotyped (when
they should be connected) for some big data sets. Maybe the same bug that
wethought we fixed in version 1.13.
- A list of haplotypes is printed to the logfile
- Close file pointer after reading sequences or after errors!
- Display messages in case haplotypes differ only by missing data
INSTALLATION
Windows
Decompress the .zip file and run the tcs.bat file.
Mac OS X
Simply decompress the .sit file. (should be done automatically upon download) Run the TCS application.
Do not move the files from the TCS package folder.
In case of problems (most often appear in Windows), repeat the full
installation again: go to the TCS page. Get JRE 1.3 (or
latest)(http://java.sun.com/j2se/1.3/jre/) and install it. Get TCS and let the unzipper
program to unzip it. You should get a folder with everything on it.
Be aware, if you have several unconnected subnetworks, TCS will not
spread those automatically. If you have overlapping haplotypes, you have to move
then around using the mouse. Nothing should overlap.
Be aware that if sequences differ only by missing data, the collapsing
to haplotypes might be ambiguous and dependent on the order of the sequences.
TCS will give an alert in such cases.
Check your data and the haplotype list in the logfile. More discussion
in the documentation
The PICT files that the programs outputs work fine in the Windows version.
In the Macintosh version they are not completely ready yet (this is being
really difficult).
And please, read the documentation.
Thank you,
David Posada (david.posada@.byu.edu)
Jacob Derington
Mark Clement
Steven Woolley
March 2003