synteny

There are 34 repositories under synteny topic.

  • tanghaibao/jcvi

    Python library to facilitate genome assembly, annotation, and comparative genomics

    Language:Python77336495189
  • pyGenomeViz

    moshi4/pyGenomeViz

    A genome visualization python package for comparative genomics

    Language:Python29735023

  • tanghaibao/quota-alignment

    Guided synteny alignment between duplicated genomes (within specified quota constraint)

    Language:Python567920

  • LyonsLab/coge

    CoGe (Comparative Genomics) Platform

    Language:Perl4483720

  • legumeinfo/gcv

    Federating genomes with love (and synteny derived from functional annotations)

    Language:TypeScript42440110

  • obenno/ShinySyn

    A shiny application to visualize MCscan result

    Language:JavaScript34228

  • orangeSi/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:HTML31507

  • dinasv/CSBFinder

    A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes

    Language:Java29324

  • Plant-Food-Research-Open/assemblyqc

    A Nextflow pipeline for evaluating assembly quality

    Language:Nextflow27131245

  • csoderlund/SyMAP

    Synteny Mapping and Analysis Program

    Language:Java26377

  • almeidasilvaf/syntenet

    An R package to infer and analyze synteny networks from protein sequences

    Language:R242166

  • lpryszcz/pyScaf

    Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.

    Language:Python2461111

  • sanger-tol/treeval

    Pipelines for the production of Treeval data

    Language:Nextflow2371785

  • tanghaibao/mcscan

    Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

    Language:C++215013

  • erinyoung/roundabout

    Finding regions of similarity between plasmids

    Language:Nextflow162110

  • jorgenunezsiri/accusyn

    AccuSyn: An Accurate Web-based Genome Synteny Browser

    Language:JavaScript16111

  • 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:Shell14014
  • Pynteny

    Robaina/Pynteny

    Query sequence database by HMMs arranged in predefined synteny structure

    Language:Python131551

  • vestalisvirginis/synphage

    Pipeline to create phage genome synteny graphics from genbank files

    Language:Python11260

  • ohdongha/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:Python9423

  • arendsee/synder

    Trace intervals between genomes using a synteny map

    Language:C++7693

  • nf-core/pairgenomealign

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

    Language:Nextflow618622

  • ksamuk/syntR

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

    Language:R5001

  • UdeM-LBIT/superrec2

    Run and compare algorithms for phylogenetic reconciliation and super-reconciliation

    Language:Python4401

  • Genome-structure-evolution-analysis/AKRUP

    AKRUP: ancestral karyotype reconstruction universal pipeline

    Language:Python3201

  • kiranbandi/mcscanx-synteny-visualizer

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

    Language:JavaScript2202

  • kullrich/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:HTML2220

  • DPP4ResearchGroup/SyntenyViz

    R package to visualize Synteny across biological species

    Language:R11310

  • jnarayan81/SyntenyParser

    Parse the syntney

    Language:Perl110

  • Robaina/Clinker_Server

    Set clinker to be run remotely from a server

    Language:PHP120

  • fg6/forACT

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

    Language:C++0202

  • ihsanmuchsin/MoSyn

    Bioinformatics pipeline for binding sites prediction

    Language:Jupyter Notebook0000

  • PalMuc/congeneric_synteny

    analysis of synteny across animals

    Language:Python00

  • TC-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:Python0100