github.com - A comparative genome scaffolding tool based on MUMmer
mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the...
pbil.univ-lyon1.fr - DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.Ancestral genes or domains are deduced from...
www.bx.psu.edu - We describe a new method for predicting the ancestral order and orientation of those intervals from their observed adjacencies in modern species. We combine the results from this method with data from chromosome painting experiments to produce a map...
www.mdpi.com - REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the...
github.com - The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc...
http://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
More at http://busco.ezlab.org/
Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput...
During recombination, the precise breakage of each strand, exchange between the strands, and sealing of the resulting recombined molecules happens. The “chromosomal breakpoints” refers to these places where they break.
4dgenome.research.chop.edu - Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted...
github.com - pyScaf orders contigs from genome assemblies utilising several types of information:
paired-end (PE) and/or mate-pair libraries (NGS-based mode)
long reads (NGS-based mode)
synteny to the genome of some related species (reference-based...