SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images. SynVisio requires two files to run:...1431 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Recip...from sequence similarity searches, codon alignments to Ka/Ks calculations and synten...1266 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
...l takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as in...block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the...936 days ago
GEnView: A phylogeny based comparative genomics software to analyze the genetic environment of genes
A phylogeny based comparative genomics software to analyze the genetic environment of genes. The user can select one...between all genomes. The sequences are then visualized, enabling comparison of synten...855 days ago
Genomicus: genome browser that enables users to navigate in genomes in several dimensions
...00 Number of extant genes 4303993 Number of ancestral species 196 Number of ancestral genes 4624213 Number of ancestral synteny blocks 83342...792 days ago
700 days ago
JBrowse 2: a modular genome browser with views of synteny and structural variation
igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fet...371 days ago
ExRec: Exclusion of Recombined DNA
ExRec (Exclusion of Recombined DNA) is a Python pipeline t...user to output the longest non-recombined sequence blocks from loci (current best practice) or randomly select non-recombined blocks from loci (a newer approach)....34 days ago