PHYLLAB is a MATLAB toolbox for sequence manipulation and phylogenetic analysis. PHYLLAB takes as input a set of aligned nucleotide or amino-acid sequences, and performs phylogeny inference. 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. Although it does not implement all the multiplicity of existing methods used in phylogenetics, interested users can extend it easily.