GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2249 days ago
DendroPy: a Python library for phylogenetic computing
...istributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipel...2217 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop a...2202 days ago
WhatsHap: fast and accurate read-based phasing
...d Individuals). WhatsHap is easy to install It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF. Supports multi-sample VCFs. It produces sta...2182 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...g tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-cov...2150 days ago
gSearch: a fast and flexible general search tool for whole-genome sequencing
gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.2111 days ago
mmgenome: Tools for extracting individual genomes from metagneomes
The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the process of ext...2108 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Gi...2107 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Mulan: Multiple-sequence local alignment and visu...d and a network server for comparing multiple draft and finished-quality...er several novel algorithms: the TBA multi-aligner program for rapid ide...ith the GALA database; alignments of multiple species dynamically genera...2094 days ago
LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now exec...pressed intermediate files. Added utilities folder. Added support for multiple short read files. Removed...2080 days ago