Software for Systematics
Tree-Search Parsimony-Based Programs: NONA and TNT
Data Management Analysis and Tree Editing: WinClada
WinClada ver. 10.00.08 updated: 29 April 2002
Downloads
WinClada
About WinClada
Program download button is at the Bottom of this page.Please read entire page before downloading).WinClada was written entirely by:Kevin C. Nixon.Copyright 1999-2002, All rights reserved.
WINCLADA Documentation
To download sample files as single self-extracting executable (run this after downloading):
To download THE SAME sample files individually (no need to do both!!!):
sample.zip
NONA
NONA IS NOW FREEWARE: DO NOT PAY FOR IT!
NONA WAS WRITTEN ENTIERLY BY:
PABLO A. GOLOBOFF
INSUE FUNDACI E INSTITUTO MIGUEL LILLO
MIGUEL LILLO 205, 4000 S. M. DE TUCUM, ARGENTINA
NONA VER 2.0 IS A WINDOWS 95/98/NT COMMAND LINE/TEXT PROGRAM THAT IS:
used to search for most parsimonious trees
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used to calculate consensus trees, etc.
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Extremely fast! In general, MUCH faster than competing software.
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WinClada is written to utilize NONA either directly as a search engine for phylogenetic analysis, or the two programs may be used separately.
NONA ver. 2.0 is now available FOR FREE
THIS VERSION IS FULLY FUNCTIONAL AND NOT IMPAIRED IN ANY WAY.
FREEWARE POLICY :
- NONA can be downloaded by anyone
TNT
What is TNT?
Tree analysis using New Technology
A new program by Pablo Goloboff, Steve Farris, and Kevin Nixon
It is a program that can:
analyse large data sets (i.e. 300-500 taxa)
in reasonable times (minutes to find a shortest tree, hours to produce a reliable consensus).
For some of the new methods already implemented in TNT, see:
Goloboff, P.A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15(4): 415-428.
Nixon, K.C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15(4): 407-414.
TNT stands for “Tree analysis using New Technology”. It is a program for phylogenetic analysis under parsimony (with very fast tree-searching algorithms; Nixon, 1999, Cladistics 15:407-406; Goloboff, 1999, Cladistics 15:407-428), as well as extensive tree handling and diagnosis capabilities. It is a joint project by Pablo Goloboff, James Farris, and Kevin Nixon.
As of November 2007, the project was subsidized by the Willi Hennig Society, and thus the program is now made freely available, upon agreement on the terms of the License. The license provided is a single-user license, and the most important requirements are that the program is not posted in other websites or mirrors, and that when publishing results you acknowledge having used the Willi Hennig Society edition of TNT and cite the paper describing the program (Goloboff et. al, 2008, in Cladistics)
Download
Warning to Vista users: you probably will have to make it run in “compatible mode” (right-clicking on the TNT icon, selecting compatibility with Windows XP) and also select “execute program as administrator”.
Note for running TNT in parallel, under Linux or Mac.- You have to install PVM3 in your machine, and copy the binary file to the PVM directory for binaries (either to $PVM_ROOT/bin/LINUX, or LINUX64, or DARWIN). Mixing 32 and 64 bit versions poses no problem, but binaries with limits on number of taxa do not connect properly to binaries without such limit, and viceversa. To avoid mixing, you can rename the binaries of any type (and make sure you copy identically renamed binaries to the corresponding PVM directory). If you have problems compiling PVM, download this file to the same directory where you have unpacked pvm3.4.5.tar.gz and expand it with tar xfvz pvm_patch.tgz, and try compilation again.
Updates.- Updates are done regularly (often every 2 months or so). The last update was done on May 11, 2008.
Documentation
The main documentation is in the file tnt.htm, and recent additions or bugfixes are in the file BugFixes.htm; both of these are contained within all the packages (except the character-mode Windows version). On-line help on all TNT commands can be obtained with the help command. A general description of the Windows version is in a QuickTutorial (a PowerPoint presentation; this is probably the easiest way to get started). The example files for scripting come in the self-extracting files zipdruns.exe or zipdruns.zip, and additional scripts (with full documentation in a pdf file) are here.
Warning/Disclaimer
Keep in mind that freezes/crashes might occassionally occur, and save results frequently. The program is intended only for strictly academic use, and is provided “as is,” with no express or implied warranties. None of the authors of TNT is responsible in any way for any problems the program causes to your computer, your data, your career, or your life. A copy of the license agreement can be found here.
Bug Reports
Bug reports are appreciated, but please keep in mind that a bug report, to be of any use, must include the version of TNT (including date), the complete data file, and all the commands necessary to show the bug (or, at least, the exact sequence of menu operations that consistently leads to a crash, freeze, or miscalculation). Send bug reports to Pablo (pablogolo@csnat.unt.edu.ar), with “tnt bug report” in the subject.
Trees
Three Gene Tree:
rbcL, atpB, 18s…
- The “three gene” tree includes 567 taxa, mostly angiosperms, with a carefully selected group of gymnosperms. For some reason, Cycads were not included.
- The shortest trees for this data set were first found with the parsimony ratchet. The Soltises approached Kevin Nixon after several months of anlayzing this data set with PAUP* on very fast Macs. They were concerned that they were not finding the shortest tree(s). The first night of running the ratchet (with DADA and NONA) on this data set (on a much slower PC), trees 12 steps shorter than had previously found were discovered. The next day, trees one additional step shorter (13 steps shorter) were found. These are almost certainly THE shortest trees for this data set. They have been verified (hit several times) with Pablo Goloboff’s new methods, sectorial searches, drift, etc., using TNT.
- We provide here a WINC file that can be loaded directly into Winclada that contains the data file (stripped of uninformative characters) and the consensus tree. Anyone wishing to have sets of individual shortest trees can send an email to the address on the homepage.
- The data/tree is stored in a single self-extracting executable. After downloading, run the executable and the file threegen.winc will be extracted. Open this file with Winclada to see/edit/play with the tree…
ZILLA
The tree you are about to link to is the REAL consensus of the shortest trees for the 500-taxon rbcL data set for seed plants that was originally published by Chase et al. (1993) and later reanalyzed by Rice et al. (1997) who was still not able to find the shortest trees for this data set.
The tree you are about to view is the ONLY public posting I am aware of (April 2002) in ANY form of the most parsimonious trees for this data set. Strangely, other sites have not acknowledged the existence of these shorter trees.
- The trees from which this consensus tree are derived are in excess of 50,000 trees
- Found with NONA using traditional searches (usually in 1-3 weeks on a 200 mhz Pentium Pro)
- Found with the ratchet (usually in 3-6 hours on a 200 mhz machine)
- These trees have a length of 16218 when uninformative characters are removed, 2 steps shorter than those found by Rice et al. (the Rice et al. trees have been verified to have 16220 steps when uninformative characters are removed, although massive confusion persists because of incorrect values reported by PAUP).
VIEW ZILLA TREE
If you want to read more about the ratchet, see:
Nixon, K. C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.
This page and tree were first posted on the web on 4 February 2000 A.D., and updated in April 2002.
