StatAlign is an free and easy to use, 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.
Requirements:
· Java 1.5 or later
What's New in This Release: [ read full changelog ]
Improvements:
· GUI update: launching an analysis requires less clicks
· New welcome message and About box
· Output files are summarised after the analysis
Bugfixes:
· RNA mode automatically disabled for non-RNA input in console mode
· Plugins that do not produce output will not create files
· Fix to allow the RNAalifold plugin to run in console mode as well
· Removed error message for input files that don't end in .fas(ta)
· PPFold fix for non-UK/US locales
· Fixed long-standing bug in Tamura-Nei model
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