synteny
There are 6 repositories under synteny topic.
tanghaibao / jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
Language:Python 702- pyGenomeViz
moshi4 / pyGenomeViz
A genome visualization python package for comparative genomics
Language:Python 232 Guided synteny alignment between duplicated genomes (within specified quota constraint)
Language:Python 54- Language:Perl 44
legumeinfo / gcv
Federating genomes with love (and synteny derived from functional annotations)
Language:TypeScript 35orangeSi / GSSplayground
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature
Language:HTML 30dinasv / CSBFinder
A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes
Language:Java 26- Language:JavaScript 26
lpryszcz / pyScaf
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
Language:Python 25csoderlund / SyMAP
Synteny Mapping and Analysis Program
Language:Java 22Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format
Language:C++ 21almeidasilvaf / syntenet
An R package to infer and analyze synteny networks from protein sequences
Language:R 18sanger-tol / treeval
Pipelines for the production of Treeval data
Language:Nextflow 17jorgenunezsiri / accusyn
AccuSyn: An Accurate Web-based Genome Synteny Browser
Language:JavaScript 16erinyoung / roundabout
Finding regions of similarity between plasmids
Language:Nextflow 14- PyntenyLanguage:Python 12
ThomasArn / genoPlotR_wrapper
Wrapper for the genoPlotR R package. This wrapper makes phylogeny, genbank files and blast comparisons that is needed for the genoPLotR package
Language:Shell 12ohdongha / OrthNet
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
Language:Python 9- Language:C++ 7
vestalisvirginis / synphage
Pipeline to create phage genome synteny graphics from genbank files
Language:Python 6- Language:R 5
UdeM-LBIT / superrec2
Run and compare algorithms for phylogenetic reconciliation and super-reconciliation
Language:Python 5Genome-structure-evolution-analysis / AKRUP
AKRUP: ancestral karyotype reconstruction universal pipeline
Language:Python 2kiranbandi / mcscanx-synteny-visualizer
A visualization tool for viewing MCscanX Synteny Collinearity files (outdated please check description or readme)
Language:JavaScript 2kullrich / CRBHits
[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.
Language:HTML 2DPP4ResearchGroup / SyntenyViz
R package to visualize Synteny across biological species
Language:R 1- Language:Perl 1
Robaina / Clinker_Server
Set clinker to be run remotely from a server
Language:PHP 1fg6 / forACT
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
Language:C++ 0ihsanmuchsin / MoSyn
Bioinformatics pipeline for binding sites prediction
Language:Jupyter Notebook 0TC-Hewitt / OatCrownRust
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.
Language:Python 0
