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