By Pavel Morozov and Andrey Rzhetsky
We developed a new toolbox (PHYLLAB) for sequence manipulation and phylogenetic analysis in MatLab (MathWorks, Inc.). PHYLLAB takes as input a set of aligned nucleotide or amino-acid sequences, and performs phylogeny inference. Besides traditional phylogenetic methods it uses a Markov chain Monte Carlo method, evaluating the posterior distribution over tree topologies and a variety of model parameters, including parameters of substitution-rate variation under a wavelet model. The graphical interface helps users to manage input data and to visualize the most likely trees; they can also view substitution-rate plots that show the maximum posterior density (confidence) intervals. PHYLLAB is written completely in the MatLab language and has been tested on WinNT platform with MatLab Version 5.3.0. Although it does not implement all the multiplicity of existing methods used in phylogenetics, interested users can extend it easily. In this manner, the PHYLLAB toolbox is continually expanding; we expect to offer many more functions and scripts for different purposes soon.
Download PhylLab manual (pdf file 532k)
PhylLab manual HTML pages are under construction now.
Also you can see related articles:
Rzhetsky, A., and P. Morozov., 2001. Markov chain Monte Carlo computation of confidence intervals for substitution-rate variation in proteins. Pacific Symposium on Biocomputing 6:203-214. PDF file (320K)
Morozov, P.S., T.L. Sitnikova,G. Churchill , F.J. Ayala , and A. Rzhetsky., 2000. A New Method for Characterizing Replacement Rate Variation in Molecular Sequences: Application of the Fourier and Wavelet Models to Drosophila and Mammalian Proteins. Genetics 154:381-395. PDF file (524K)