BOL

github.com - Progressive Cactus is a whole-genome alignment package. Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules https://github.com/glennhickey/progressiveCactus

www.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...

github.com - Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

github.com - Typically in comparative genomics, we can identify anchors, chain them into syntenic blocks and interpret these blocks as derived from a common descent. However, when comparing two genomes undergone ancient genome duplications (plant genomes in...

github.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...

www.ncbi.nlm.nih.gov - Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional...

github.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...

bioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...

github.com - BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and...

www.biostat.wisc.edu - Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an...