Models of nucleotide or amino acid sequence evolution that implement homogeneous and stationary Markov processes of substitutions are mathematically convenient but are unlikely to represent the true complexity of evolution. With the large amounts of data that next generation sequencing promises, appropriate models of evolution are important, particularly… (More)
SUMMARY SQUINT is a sequence alignment tool, and combines both automated progressive sequence alignment with facilities for manual editing. The program imports nucleotide or amino acid sequence multiple alignment files in standard formats, and permits users to view two translations of the same multiple alignment simultaneously. Edits in one view are… (More)
The Phylogenetic Analysis Library (PAL) is a Java class library for performing phylogenetic inference and analysis of primarily molecular sequence data. In this paper the features of PAL are described, in particular the new features since version 1.1. Practical examples of the usage of PAL are also given.