Software obligatorio para el curso de la Universidad de La Habana
ClustalX: The paradigmatic alignment software.
ClustalX Help: A very detailed user's guide to ClustalX. Versions available for all platforms.
BioEdit: A free alternative to Sequencher. Windows OS only. Runs Clustal, translates DNA to amino acid sequence, calculates reverse complement, and reads raw chromatograms.
MEGA version 3, for Windows OS.
dnaSP: the industry standard for population genetic analysis of DNA sequences. For Windows OS.
IM (Isolation with Migration model analysis using MCMC)
IM: Assuming two recently separated populations/species, estimates effective pop. sizes (including the common ancestor's), asymmetric migration rates, divergence time, and relative sizes of the two founding populations. For Windows/DOS or Unix (Darwin or Linux).
IM documentation dated 24 October 2005, in PDF.
Nested Clade (Phylogeographic) Analysis
The official network-building software for NCPA is TCS. We will certainly need GeoDis. These programs and the latest NCPA inference key should be available on David Posada's webpage. In our lab we will also try a much friendlier program for making networks, called Network 220.127.116.11.
For many software programs one needs to be sure that Java is installed on the computer.
We will need at least Java Virtual Machine version 1.4.2.
You can automatically get Java here, or check which version of Java you have by clicking here. You can also check by typing at the Command Prompt (Símbolo del Sistema)java -version.
PAUP* - SADLY, IT IS NOT FREE
We will bring copies of this software. For more information check the PAUP* FAQ. And download but do not bother printing the PAUP* commands reference version 2, as PDF. A new version of PAUP* should be released any time now...
Also look at these suggestions from Swofford for running a good first set of analyses using PAUP*.
And be sure to see Brian O'Meara's PAUP* instructions: the best on-line resource for using PAUP*, especially for running batch files.
More free software from David Posada: Modeltest.
Software adicional que podría ser interesante para l@s estudiantes
Mesquite: Includes modules for coalescent simulations, as well as manipulating & visualizing alignments. Calculates the reverse & complement of a DNA sequence, which the new MacClade does not. MAC only.
BayesPhylogenies: a powerful alternative to MrBayes by Pagel & Meade. BayesPhylogenies implements "mixture models": the user decides how many partitions to implement and the software estimates in what proportion each partition applies to each site. Remarkable!
MrBayes, download the latest version.
A forum for MrBayes users.
Tracer, a very useful program for visualizing and evaluating the quality of Bayesian MCMC analyses.
seq-gen, version 1.3: for simulating the evolution of DNA sequences on a given tree. Also by Andrew Rambaut.
DIVERGENCE TIME ESTIMATION
multidivtime, Bayesian MCMC analysis of divergence time without assuming a 'molecular clock.'
BEAST, another Bayesian analysis of divergence time without assuming a 'molecular clock.'
PaupUP is free software to convert the DOS (not Windows™ OS) version of PAUP* into a point-and-click menu and window driven version. See Screenshot. 80% of PAUP*'s commands are available via the menus, the other 20% are still accessible via the command line. The software also incorporates features of Modeltest and TreeView.
MORE USEFUL PAGES
PhyCom: An excellent forum for keeping up with the latest developments in phylogenetics. Check it frequently!
Genetics Software Forum: Questions and answers for users of various evolutionary genetic software packages.
This page will be growing constantly, because there are always new software packages...