Bayesian Evolutionary Analysis Sampling Trees (BEAST) is a program for Bayesian Markov Chain Monte Carlo (MCMC) analysis of molecular sequences. It is oriented towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between genetic sequences, comparing nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
ClustalW2, ClustallW, and ClustalX are general purpose, multiple sequence alignment tools. Multiple alignments of protein sequences can identify conserved sequence regions. This is useful in designing experiments to test and modify the function of specific proteins, in predicting the function and structure of proteins and in identifying new members of protein families. Clustal is a general purpose multiple sequence alignment program for DNA or proteins.
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include: parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Input data types include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.