Distribution-specific packages will be available in the next couple of days
PLL - Phylogenetic Likelihood Library
PLL is a highly optimized, parallized software library to ease the development of new software tools dealing with phylogenetic inference.
Among the functions included in PLL are parsing multiple sequence alignments (MSA) from PHYLIP and FASTA files, reading Newick trees, performing topological moves such as SPR and NNI, model optimization, likelihood evaluation and partitioned analysis by assigning different substitution models to each partition of the MSA. PLL fully implements the GTR nucleotide substitution model for DNA data and a number of models for aminoacid data.