Software

MIPS PlantsDB CrowsNest

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.

REPET

The REPET package (Flutre et al, 2011) integrates bioinformatics programs in order to tackle biological issues at the genomic scale.

S-MART

S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.
S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.

VANTED

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.

LAILAPS

LAILAPS is information retrieval system for all kinds of biological and life science databases. It is used to search and extract relevant content from dozend of databases. The entries are ranked for their relevance in consideration of the users individual preferences.

MAPHiTS: Mapping Analysis Pipeline for High-Throughput Sequences

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.

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