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.

 

OUTPUT GRAPHS

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.

 

 

MISSING DATA

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

 

PICT files

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