Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints

analysis of synteny across animals

Bioinformatics pipeline for binding sites prediction

Custom scripts and workflows used in the genomics and population analysis of oat crown rust (Puccinia coronata f. sp. avenae) preprint (bioRxiv 2023.09.18.557855). All steps performed in Linux environment or R.

Set clinker to be run remotely from a server

R package to visualize Synteny across biological species

phylogeny and collinearity aware assembly evaluation toolkit.

SCANS pipeline to identify orthologous lncRNAs between species using synteny and sequence alignment analysis.

A visualization tool for viewing MCscanX Synteny Collinearity files (outdated please check description or readme)

Python pipeline for automated synteny block detection and visualization from multiple genomes.

Parse the syntney

AKRUP: ancestral karyotype reconstruction universal pipeline

Run and compare algorithms for phylogenetic reconciliation and super-reconciliation

CRBHits - a reimplementation of the Conditional Reciprocal Best Hit algorithm in R.

R package for the reproducible detection of synteny blocks using genetic map data

Trace intervals between genomes using a synteny map

A visualization tool for studying chromosomal rearrangements through interactive synteny block analysis and chromosome breakpoint mapping.

CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

Query sequence database by HMMs arranged in predefined synteny structure