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github.com - SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web. More at http://sequenceserver.com.

github.com - Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive...

github.com - TMAP - torrent mapping alignment program General Notes TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies. The latest TMAP is unsupported. To use a...

lifemap-ncbi.univ-lyon1.fr - Lifemap is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in Lifemap is similar to the one used in cartography with tools like Google Maps© or Open Street Maps: exploring is done by zooming and panning.  The...

compbio.mit.edu - ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial...

amp.pharm.mssm.edu - Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse...

www.baseclear.com - SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or...

www.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...

We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation...

github.com - Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...