Software

A list of available software packages.

SHOGUN: Large-scale Machine Learning Toolbox
PALMapper: RNA-Seq short read aligner program
mGene: A computational tool for accurate genome-wide prediction of genes from DNA sequences
rQuant: A tool for transcriptome quantitation from RNA-seq experiments
KIRMES: Kernel-based Identification of Regulatory Modules in Euchromatic Sequences
EasySVM: A set of tools based on the Shogun toolbox allowing to train and test SVMs in a simple way
ARTS: A tool for Accurate Recognition of Transcription Starts in Human
ASP: A program to predict accurate splice sites on genomic sequences of several organisms
QPALMA: Aligning spliced reads produced by Next generation sequencing technologies

News: The group will join the Sloan-Kettering Institute in New York City in January 2012 Oct 25, 2011; Paper on Transfer Learning and Sequence Segmentation accepted at NIPS'11 Oct 23, 2011; The Labor Journal writes about the Web Service Study in an Editorial Oct 23, 2011; Paper on the Analysis of 19 Genomes and Transcriptomes of Arabidopsis thaliana has been published in Nature Aug 28, 2011; PLoS ONE accepts publication on Persistence and Availability of Web Services in Computational Biology Aug 23, 2011; Best Oral Presentation Award Runner Up presented to Sebastian J. Schultheiss at SCS7 Jul 17, 2011; Best paper award for paper on transfer learning Jul 03, 2011; Simple Alignment Filtering Tool (SAFT) released Jun 08, 2011; More news…