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:
- Fixed bug that prevented PICT or PS output
- Fixed a bug that resulted in incorrect connections in some special cases.
- Improved the PICT output format.
- Removed the nesting option, which was available by mistake.
- Allow users to select the confidence level for the parsimony limit.
- Added option to automatically select the root (assumes root is the rectangular node).
- Improved GUI.
- The program can read IUPAC symbols and will treat them as missing data.
- Fixed other minor bugs
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
- Windows: The latest version of Java, 1.4.2 works fine
- Unix-like: The latest version of Java, 1.4.2 should work fine
- MacOS X: Here there is an issue with repainting in Java 1.4.2 (which is installed by default in Mac OS 10.3), so an executable file provided is forced to run under Java 1.3.1 . It is possible that the program will run correctly under java 1.4.1 in MacOS X. In general, java versions available under MacOS X can be seen under /System/Library/Frameworks/JavaVM.framework/Versions/
How to start TCS
- Windows: double click on the TCS.1.17.jar file.
- Unix-like: double click on the TCS.1.17.jar file or type "java -jar TCS1.17.jar" in a terminal window after moving to the TCS directory.
- MacOS X: double click on the TCS1.17mac.app file, which forces the app to run under java 1.3 (the jar file will run too in a mac, but if java 1.4.2 is installed the graph canvas will appear black). This application will not run under MacOS 9.
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 "TCS1.17.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