Software and Data

Tools for biodiversity assessment

  • bagpipe    BAGpipe (Copyright © Anna Papadopoulou, Douglas Chesters & Jesús Gómez-Zurita): Pipeline for Biodiversity Assessment using GenBank data

Tools for molecular evolution, phylogenetics and phylogenomics 

  •  bfca  Bfca (Copyright @ Carmelo Andújar, Víctor Soria-Carrasco & Jesús Gómez-Zurita): Bayes Factor Cluster Analysis, for selection of consistent calibration hypothesis for molecular clock analyses

  • gblocks_icon   GBlocks (Copyright © Jose Castresana): Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

  • ktreedist_icon   Ktreedist (Copyright © Víctor Soria-Carrasco & Jose Castresana): Calculation of the minimum branch length distance (K tree score) between phylogenetic trees  

  •  IRiSpic  IRIS (Identifying Recombination in Sequences)  IRiS is a tool to detect historical recombination events. IRiS is able to  detect    the breakpoint location, the ancestral haplotypes and the descendant sequences of past recombination events by analyzing a set of extant sequences. It has been extensively calibrated to be run in human sequences.

 Tools for SNP genotyping

  •  SNPatorSNPator (created by CEGEN-UPF and INB-UPF): A tool to make the management and analysis of genomic SNP data. Tipical quality control and statistical procedures can be performed in an easy and quick way even by people with no deep IT knowledge

  • lSYSNPslogoSYSNPs (created by  INB-UPF): First web server implementing algorithms that allow for efficient and simultaneous consideration of all the relevant criteria in order to obtain tag-SNPs that appropriately cover large sets of genes, genomic regions or Gene Ontology (GO) terms.

Tools for Copy Number Analysis

  • CHAVACHAVA (Copyright © Carlos Morcillo) is a java based visual application conceived to estimate CNV regions from CGH data using a HMM model. CHAVA allows the user to easily navigate and zoom along all the data and change the HMM parameters used in the CNV estimation to search for maximum consistency between direct and swap dyes in the CGH experiment.