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.

It comes in three flavours — single-thread, POSIX Threads, and MPI. Each version is optimized for the Streaming SIMD Extensions 3 (SSE3) and Advanced Vector Extensions (AVX).

Latest News

Version 1.0.2 released


Version 1.0.2 includes a number of new models, and improvements

Version 1.0.0 released


The first version of PLL is finally available. It is available as a standalone library and in source code format.

PLL comes in a number of flavors, from simple, single-thread library to multi-thread and MPI based with a number of hardware optimizations. It is also to make use of a number of hardware-based optimizations such as SSE3 and AVX instruction set.