HyPhy (Hypothesis testing using Phylogenies,) is a mature (in development since 1997), feature rich, scriptable and fast maximum likelihood sequence analysis software platform.
HyPhy has over 5000 registered users and over 400 citations in peer reviewed literature.
Here are some key features of "HyPhy":
· Positive and negative selection detection
· Recombination analysis
· Detecting co-evolving residues
· Genomic and multiple-gene evolutionary inference
· Molecular clock and relative rate tests
· Nucleotide, protein and codon model selection
· As a likelihood analysis engine for other software and web services
· One-off analyses: tasks that no other package does out of the box and are not worth writing a specialized program for