LANE runner is a JAVA application developed to facilitate the annotation of de novo sequenced transcriptomes. It was extensively used for the project and for building the subsequent database. ‘LANE runner 2.0’ integrates:
- Iterative BLAST+ searches (Camacho et al. 2009) against multiple databases,
- Reciprocal Best BLAST Hits (RBBH) identification for homology assessment, and
- Consensus sequence building to assemble sequences exhibiting the same annotation.
MANTiS is an application system that: builds a relational database integrating, in a phylogenetic framework, all Ensembl genes, corresponding PANTHER molecular functions and biological processes, as well as GNF, e-genetics, and HMDEG expression data; makes extensively use of the Ensembl ortholog/paralog prediction pipeline for identifying gene duplication events; and implements a dynamical programming approach for the mapping of gene gains, duplications, and losses on the phylogenetic tree.
MetaPIGA is a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood). It includes a random-restart hill climbing, a simulated annealing algorithm, a classical genetic algorithm, and the metapopulation genetic algorithm (metaGA). MetaPIGA allows the use of morphological (presence/absence) and molecular (DNA, Proteins) data.