bioinfo.konkuk.ac.kr - Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC...
github.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111
Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...
github.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)
Link to working demo:...
github.com - A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat)
This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]
github.com - To create a fresh environment for chromatiblock to run in do:
conda create --name chromatiblock
conda activate chromatiblock
conda install chromatiblock --channel conda-forge --channel bioconda
Then in future to run chromatiblock you can...
github.com - RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This...
almob.biomedcentral.com - Background
The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of...
code.google.com - Perl module for creating geographic 10km-square maps using either SVG or PNG (with GD library) output format.
Originally design to map the location of objects in a 10 km map IrishGrid includes:
native support of the Irish Grid System (see...
http://shinyheatmap.com/ - Background: Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets. Visualizing such big data has posed technical challenges in biology, both in...
github.com - JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl.
Headline Features:
Fast, smooth scrolling and zooming. Explore your genome with unparalleled...
