Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
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Updated
May 24, 2020 - C++
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
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
A visualization tool for viewing MCscanX Synteny Collinearity files (outdated please check description or readme)
AKRUP: ancestral karyotype reconstruction universal pipeline
[CRBHits](https://github.com/kullrich/CRBHits) is a reimplementation of the Conditional Reciprocal Best Hit algorithm [crb-blast](https://github.com/cboursnell/crb-blast) in R.
Run and compare algorithms for phylogenetic reconciliation and super-reconciliation
R package for the reproducible detection of synteny blocks using genetic map data
Pipeline to create phage genome synteny graphics from genbank files
Trace intervals between genomes using a synteny map
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
Query sequence database by HMMs arranged in predefined synteny structure
Finding regions of similarity between plasmids
AccuSyn: An Accurate Web-based Genome Synteny Browser
An R package to infer and analyze synteny networks from protein sequences
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