PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using...same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENC...841 days ago
2038 days ago
VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).2006 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
Synima written in Perl, which uses the graphical features of R. Synima takes orthologu...LAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these program...2006 days ago
1531 days ago
Synteny and Rearrangement Identifier (SyRI)
SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-geno...1453 days ago
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...1427 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 reim...from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package targets ec...1262 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tre...932 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...etween all genomes. The sequences are then visualized, enabling comparison of synteny and gene content. More at&nb...851 days ago