Useful tools

LANE runner is a JAVA application developed to facilitate the annotation of de novo sequenced transcriptomes. It was extensively used for the Reptilian Brain Transcriptome project and for building the subsequent Reptilian Transcriptomes 2.0 database. ‘LANE runner 2.0’ integrates:

1. Iterative BLAST+ searches (Camacho et al. 2009) against multiple databases,
2. Reciprocal Best BLAST Hits (RBBH) identification for homology assessment, and
3. Consensus sequence building to assemble sequences exhibiting the same annotation.

DISCONTINUED! 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.