(Weighted) Probabilistic substitution mapping – Compute all (weighted) number of substitutions occurring on each branch of a tree, for each site of an alignment.
Co-evolution analysis – Using the substitution mapping, look for significantly groups of sites departing the null hypothesis of independence. Two kind of analyzes are provided: a pairwise analysis, presented in Dutheil et al. (2005), and a clustering analysis in Dutheil and Galtier (2007). In both cases, a parametric bootstrap approach is used to evaluate the significance of groups. Simulation results are written to separate files, a statistics software like R is required to look for the significance.
GenGIS is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.
xMAN (extreme MApping of OligoNucleotides) is a simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length. xMAN is at least an order of magnitude faster than other popular existing tools.
CREST (clipping reveals structure) is an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution.
MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.
rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.
PLABQTL (PLAnt Breeding QTL analysis)is a program written for the detection of loci which affect the variation of quantitative traits. Its main purpose is to localize and characterize QTL (Quantitative