(16) Application of Parallel Logic Programming for Reconstruction of Molecular Phylogenetic Trees using the Maximum Likelihood Method

DeepForest is a set of predicates to analyze molecular data (amino acid and nucleotide sequences) in respect of molecular evolution. Function of DeepForest can be divided into three parts, inference of molecular phylogenetic trees, multiple alignment, and database operation. Full set of DeepForest(Unfortunately, the full set version is not released now.) not only analyzes sequence data, but also interprets generated phylogenetic trees to extract significant information. On the other hand, DeepForest includes a set of utility programs (strictly speaking, they are predicates). They search and read input data, convert formats, write output data, and make bibliographies. They are all written in KL1, and can run on usual UNIX machines with KLIC. We tested these programs on various machines, from Macintosh to CRAY CS6400. DeepForest was designed to provide useful predicates rather than a package program. We hope users to understand KL1, and write their programs using DeepForest. Although KL1 is nothing but logic programming, it is very easier to learn than PROLOG.