Basal classes and utilities. Exceptions, text and file manipulation.
Numerical calculus. Vector and matrix manipulation, optimization, algebra,
probability distribution and statistics, random number generation.
Sequence manipulation, alphabets, chemical properties and distances,
input/output in various formats (Fasta, Phylip, Clustal, etc.).
Phylogenetics. Tree reconstruction by maximum parsimony, distance methods or maximum likelihood,
parameter estimations, ancestral states reconstruction, etc.
Population genetics. Polymorphism statistics,
linkage desequilibrium, neutrality tests and recombination.