Bioinformatics Tools
We developed and mantain the following bioinformatics tools:
The EPIGEN-SW is implemented as a web tool and facilitates the access to computational resources through an integrative and interactive approach based on flowcharts, masterscripts and auxiliary scripts. (To appear)
DANCE is a graph-based web tool that allows to integrate and visualize information on human complex phenotypes and their GWAS-hits, as well as their risk allele frequencies in different populations. (Araújo et al., 2015)
CNVice (Inbreeding Coefficients Estimation for CNV data) is a freely available R script for population genetics applications. (To appear)
DIVERGENOME is a bioinformatics platform to assist population genetics and genetic epidemiology studies performed by small- to medium-sized research groups. The platform manages a relational database where information on genotypes, polymorphism, laboratory protocols, individuals, populations, and phenotypes is organized in user projects. (Magalhães et al., 2012)
DIVERGENOMEtools is a set of tools to convert data formats as required by popular software in population genetics and genetic epidemiology. It implements a new method proposed by our laboratory. It consists of a graph-based approach to compose pipelines automatically by compiling a specialised set of tools on demand, depending on the functionality required, instead of specifying every sequence of tools in advance. (Rodrigues et al., 2012)
Implements a pipeline that facilitates data handling typical of re-sequencing studies. Functionalities: (1) consolidates different outputs produced by distinct Phred-Phrap-Consed contigs sharing a reference sequence; (2) checks for genotyping inconsistencies; (3) reformats genotyping data produced by Polyphred into a matrix of genotypes with individuals as rows and segregating sites as columns; (4) prepares input files for haplotype inferences using the popular software PHASE; and (5) handles PHASE output files that contain only polymorphic sites to reconstruct the inferred haplotypes including polymorphic and monomorphic sites as required by population genetics software for re-sequencing data such as DNAsp. (Machado et al., 2011)