TCS1.21 network relationship

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TCS 1.21 (30 June 2005)

2000-2005 © Mark Clement, Jacob Derington (Brigham Young University, USA)

DISCLAIMER

This program is free software; you can redistribute it and/or modify it under the terms of the GNU

General Public License as published by the Free Software Foundation; either version 2 of the

License, or (at your option) any later version. This program is distributed in the hope that it will be

useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY

or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not,

write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,

USA.

Version 1.19 (23 April 2005): Fixed potential printing bug at TextOutputStream.java. It should not

Version 1.18 (June 2004): Fixed gapmode, the program was always ignoring gaps (thanks to Manel

Version 1.17 (May 2004): Fixed bug that prevented PICT or PS output. Small code reorganization

Version 1-14-1.16 (May 2004): (many fixes were done since the last distributed version; complete

Version 1.06: several cosmetic changes and some bugs fixed

Version 1.02: outgroup weights estimation included

Version 1.01: distances file included

Version 1.00: First version of the program.

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PROGRAM CITATION

Clement, M., D. Posada and K. A. Crandall 2000. TCS: a computer program to estimate gene

genealogies. Molecular Ecology 9 (10): 1657-1660.

2) Or in a terminal window, type “java –version”.

The JVM is included also in:

More information on obtaining the JVM in: http://java.sun.com/

To automatically download the JVM: http://java.sun.com/webapps/getjava/BrowserRedirect

After Java is properly installed, to run TCS you should not have to do nothing other than decompress

the compressed distribution files. Just use the executables file in the bin folder. Do not change the

location of the different files within the program folder.

Suggestion (from Christoph Held) for Windows:

1) Create a directory somewhere you like and name it e.g. "TCS".

2) Unzip the content of the file you have downloaded to this directory

(tick the option "use folder names" or similar in your zip program to

maintain the directory structure of TCS. No further installation steps

are needed.

Program in its options tab.

BACKGROUND

TCS is a computer program that implements the estimation of gene genealogies from DNA

sequences as described by (Templeton et al. 1992). This cladogram estimation method is also

known as statistical parsimony. Some useful references are indicated below.

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The probability of parsimony (as defined in Templeton et al. [1992], equations 6, 7, and 8) is

calculated for DNA pairwise differences until the probability exceeds, by default, 0.95. The number

Note: TCS is not for RFLPs

TCS calculations for the probability of parsimony are only for DNA sequence data. If your data is

RFLPs you might think you could input absolute distances, but that would not work. The problem is

that for each pair of RFLP haplotypes, the parsimony connection limit could be different, depending

on the number of shared sites. This is because for RFLPs the total number of characters minus the

number of characters with a different state does not necessarily equal the number of shared

characters (which is true for DNA sequences). The difference with DNA sequences is that ++ is a

shared site, while -- is not a shared site. But you could build an RFLP network by hand.

PROGRAM FILES

Input files

The TCS software works with aligned nucleotide sequence. It opens DNA alignment files in either

which correlate with haplotype age (Donnelly and Tavaré 1986; Castelloe and Templeton 1994).

Some examples:

Aligned DNA sequences

This is sequential NEXUS:

#NEXUS

Begin data;

Dimensions ntax=4 nchar=6;

Format datatype=nucleotide gap=- missing=? ;

Matrix

Seq1 AAAAA-

Seq2 AAAAC-

Seq3 AAAAA?

Seq4 AAAAAA

;

Seq2 AAAAC-

Seq3 AAAAA?

Seq4 AAAAAA