Here, I summarized a random set of useful links toward software, programming libraries and scientific projects that I like:
APE is a set of R functions dedicated to phylogenetic analyses, including plotting tree and comparative analysis.
Bio++ is an ever-growing C++ library for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics.
Coevol is a Bayesian MCMC software for comparative analyses combining molecular data and continuous characters (e.g., ecological variables or life-history traits)
A very nice suite of programs designed for all kinds of sequences handling, sequences analyses and much more...
Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons.
Database of orthologous sequences in mammals.