Table 1 Libraries available and dependencies.

Utils

Basal classes and utilities. Exceptions, text and file manipulation.

NumCalc

Numerical calculus. Vector and matrix manipulation, optimization, algebra,

probability distribution and statistics, random number generation.

SeqLib

Sequence manipulation, alphabets, chemical properties and distances,

input/output in various formats (Fasta, Phylip, Clustal, etc.).

PhylLib

Phylogenetics. Tree reconstruction by maximum parsimony, distance methods or maximum likelihood,

parameter estimations, ancestral states reconstruction, etc.

PopGenLib

Population genetics. Polymorphism statistics,

linkage desequilibrium, neutrality tests and recombination.