CoBiG²

CoBiG2 aim is to implement population genomics approaches to study the evolutionary and ecological diversification of species in natural environments and to study the genomic process of adaptation of organism and populations to their environments. Additionally we also aim to carry out associations studies between traits and genotypes and how they can very under different environmental conditions. Both aims are particular relevant for forecasting the impact of environmental changes on natural populations as well as for implementation of marker-assisted selection. Understanding the genetics and genomics of the environmental change and its consequences for biodiversity and its preservation is the overall goal of this research group.

In close interaction with the above work and goals, third-party and in-house developed software, bioinformatics pipelines and data mining computational techniques are used to analyze the generated population-genetic, phylogenetic, and phylogeographic datasets. A more recent challenge in this direction is the analysis of the large datasets that we are about to generate using next-generation sequencing technology under a population genomics and gene discovery framework, to address the scientific questions above.

NCBI Mass Downloader

  • Posted on: 11 May 2017
  • By: bcosta

Large dataset downloading made easy

Sequence databases, such as NCBI, are a very important resource in many areas of science. Downloading small amounts of sequences to local storage can easily be performed using any recent web browser, but downloading tens of thousands of sequences is not as simple.

4Pipe4

  • Posted on: 11 May 2017
  • By: bcosta

A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information

Structure_threader

  • Posted on: 11 May 2017
  • By: bcosta

A wrapper program to parallelize and automate runs of "Structure", "fastStructure" and "MavericK".
Furthermore, Structure_threader further extends on the parallelization by also automating the estimation of "K", and the MeanQ plotting. These are outputted in 2 formats, a typical vectorial format, of "publication quality" plots, and a new, interactive plot, which is particularly suited for data exploration.