CrowsNest is a tool to interactively visualize and investigate syntenic relationships between (monocot) genomes at macro and micro levels. It allows to intuitively explore rearrangements, inversions, deletions at different resolutions, to transfer knowledge about function and conservation between several plant species and to derive evolutionary information.

This system makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies. It is possible to map experimental datasets onto the graph elements and visualize time series data or data of different genotypes or environmental conditions in the context of a the underlying biological processes.

The MAPHiTS pipeline allows the detection of single nucleotide polymorphisms (SNPs) and small insertion/deletions (indels) by comparing high-throughput Illumina short-reads (GAIIx or HighSeq) with a reference sequence from the same or a different species. This pipeline is based on public softwares (BWA, Bowtie, SAMtools, VarScan and Tablet) and homemade tools. In particular, we developed tools to filter out short-reads of low quality and to prepare the mapping and SNP calling.