Statalign

StatAlign: an extendable software package for Bayesian analysis of protein, DNA and RNA sequences.

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 quantification of the uncertainty in these estimates.

This approach accounts for the inherent interdependence between estimation of alignments and phylogenies, avoiding the inherent bias present in traditional methods that rely on a single alignment. This helps to avoid artifacts such as those resulting from the choice of guide tree when constructing alignments.

The models behind the analysis permit the comparison of evolutionarily distant sequences. The TKF92 insertion-deletion model allows for indel information to be used to help inform phylogeny estimation, and can be coupled with a wide variety of substitution models. A broad range of models for nucleotide and amino acid data is included in the package and the plugin management system ensures that new models can be easily added.

Manual: here

Input files: StatAlign accepts Fasta format alignments.

Output files:

The table below shows the kinds of results returned by CIPRES Science Gateway:

Input File Names Sample File from a Test
sequence file infile.txt
tree file treefile.tre
   
Sample Output File Type File Name
log file useTree3.log
tree file(s) useTree3.tree
tree II useTree3.ll
tree lengths useTree3.length
Model params useTree3.coreModel.params
Model params stdout.txt

If you use StatAlign here, please cite:

Novák Á, Miklós I, Lyngsø R and Hein J (2008) StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics, 24(20):2403-2404.

Arunapuram P, Edvardsson I, Golden M, Anderson JWJ, Novák Á, Sükösd Z and Hein J (2013) StatAlign 2.0: Combining statistical alignment with RNA secondary structure prediction. Bioinformatics, 29(5):654-655.

If there is a tool or a feature you need, please let us know.

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