StatAlign
(c) 2008 Ádám Novák, István Miklós, Rune Lyngsoe, Jotun Hein
StatAlign is an extendable software package for Bayesian
analysis of Protein, DNA and RNA sequences.
Multiple alignments, phylogenetic trees and evolutionary parameters
are co-estimated in a Markov Chain Monte Carlo framework, allowing
for reliable measurement of the accuracy of the results.
This approach eliminates common artifacts that traditional methods
suffer from, at the cost of increased computational time. These
artifacts include the dependency of the constructed phylogeny on a
single (probably suboptimal) alignment and bias towards the guide
tree upon which the alignment relies.
The models behind the analysis permit the comparison of evolutionarily
distant sequences: the TKF92 insertion-deletion model can be coupled
to an arbitrary substitution model. A broad range of models for
nucleotide and amino acid data is included in the package and the
plug-in management system ensures that new models can be easily added.
StatAlign is written in Java 1.5. No installation is needed to run the program, but you must have
a Java Virtual Machine (JVM) 1.5 or higher installed. If you do not have such a JVM on your
computer, please, visit www.sun.com for a free download.
The package with full documentation and source code can be downloaded from here. The downloaded file is a tar.gz file. Under Windows operating system, you can uncompress this using WinRAR. Under Linux/Unix, use the command
In Mac OS/X, just double-click the icon in Finder, and Finder will automatically decompress the package.
The package contains the source code in the src/ folder, the binaries in the bin/ folder, documentation in the doc/ folder and some auxiliary data in a few other folders (e.g. you will find nice sample sequence files in the data/ folder).
The easiest way to run the program is by
clicking the jar file which is included in the package.
You can also run the program from command line. To do so,
change directory to bin/, and type
If you would like to download the jar file only (contains everything you need for running the program, including documentation but no source code), use this link.
The help page of the program is available from
here
The help page for developers is available from
here
The documentation of the classes can be found here
or without frames here