TCS 1.16 readme


Updates

Many fixes were done since the last distributed version (version 1.13). More details are given in the documentation and at the beggining of the file dna.java. The more relevant fixes were:

Requirements

To run TCS, a Java Virtual Machine (JVM) has to be properly installed in your system. To test your JVM The JVM is included also in on the Java Runtime Environment (JRE) or the Java 2 Platform Standard Edition (J2SE). More information on obtaining the JVM at http://java.sun.com. To automatically download the JVM at http://java.sun.com/webapps/getjava/BrowserRedirect

How to start TCS


Input files

TCS will accept an alignment of DNA sequences in NEXUS sequential (example.nex) or PHYLIP sequential (example.phy) format. If needed, the program will automatically collapse the sequences into unique haplotypes and then proceed to the cladogram estimation. Example files are provided under the "sample" directory.

Output files

It will save a graph (dataname.graph) that it can be opened later. Note that if there are several unconnected subnetworks, TCS will not spread those automatically. If there are overlapping haplotypes in the resulting graph, the user will need to move then around using the mouse. Nothing should overlap at the end. Note that the lenght of the branches is meaningless here, they alwaus imply one difference.

Missing data

If some sequences differ only by missing data, collapsing to haplotypes might be ambiguous and dependent on the order of the sequences. TCS will give an alert in such cases. Check the data and the haplotype list in the logfile. More discussion in the documentation

Documentation

Detailed documentation describing TCS usage is included in the file "TCS1.16.html" under the directory "docs". This file can be open directly by double-clicking or accessed through the menu "TCS" if the directory structure is preserved.

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. See the file "gpl.html" under the "license" directory.

David Posada (dposada@uvigo.es) May 2004