Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: synteny
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
Language: Python - Size: 9.35 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 692 - Forks: 179
csoderlund/SyMAP
Synteny Mapping and Analysis Program
Language: Java - Size: 142 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 20 - Forks: 7
sanger-tol/treeval
Pipelines for the production of Treeval data
Language: Nextflow - Size: 48.8 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 17 - Forks: 3
moshi4/pyGenomeViz
A genome visualization python package for comparative genomics
Language: Python - Size: 47.8 MB - Last synced: 17 days ago - Pushed: 6 months ago - Stars: 227 - Forks: 20
almeidasilvaf/syntenet
An R package to infer and analyze synteny networks from protein sequences
Language: R - Size: 75 MB - Last synced: 3 days ago - Pushed: about 1 month ago - Stars: 18 - Forks: 6
LyonsLab/coge
CoGe (Comparative Genomics) Platform
Language: Perl - Size: 162 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 44 - Forks: 17
lpryszcz/pyScaf
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
Language: Python - Size: 3.07 MB - Last synced: 12 days ago - Pushed: over 5 years ago - Stars: 24 - Forks: 11
vestalisvirginis/synphage
Pipeline to create phage genome synteny graphics from genbank files
Language: Python - Size: 3.47 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 0
tanghaibao/quota-alignment
Guided synteny alignment between duplicated genomes (within specified quota constraint)
Language: Python - Size: 2.96 MB - Last synced: about 16 hours ago - Pushed: over 6 years ago - Stars: 54 - Forks: 21
Robaina/Pynteny
Query sequence database by HMMs arranged in predefined synteny structure
Language: Python - Size: 22.1 MB - Last synced: 19 days ago - Pushed: 6 months ago - Stars: 12 - Forks: 1
arendsee/synder
Trace intervals between genomes using a synteny map
Language: C++ - Size: 4.52 MB - Last synced: 6 months ago - Pushed: about 5 years ago - Stars: 7 - Forks: 3
fg6/forACT
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
Language: C++ - Size: 11.6 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 2
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 - Size: 389 KB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 11 - Forks: 4
Genome-structure-evolution-analysis/AKRUP
AKRUP: ancestral karyotype reconstruction universal pipeline
Language: Python - Size: 35.6 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 2 - Forks: 1
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: HTML - Size: 148 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 27 - Forks: 7
ksamuk/syntR
R package for the reproducible detection of synteny blocks using genetic map data
Language: R - Size: 2.3 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 4 - Forks: 1
legumeinfo/gcv
Federating genomes with love (and synteny derived from functional annotations)
Language: TypeScript - Size: 13.5 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 30 - Forks: 12
UdeM-LBIT/superrec2
Run and compare algorithms for phylogenetic reconciliation and super-reconciliation
Language: Python - Size: 688 KB - Last synced: about 13 hours ago - Pushed: 30 days ago - Stars: 5 - Forks: 1
tanghaibao/mcscan 📦
Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format
Language: C++ - Size: 27.9 MB - Last synced: 6 months ago - Pushed: over 13 years ago - Stars: 21 - Forks: 12
jorgenunezsiri/accusyn
AccuSyn: An Accurate Web-based Genome Synteny Browser
Language: JavaScript - Size: 31.8 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 14 - Forks: 2
erinyoung/roundabout
Finding regions of similarity between plasmids
Language: Nextflow - Size: 1.15 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0
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: HTML - Size: 71.5 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 1 - Forks: 0
obenno/ShinySyn
A shiny application to visualize MCscan result
Language: JavaScript - Size: 14 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 11 - Forks: 5
dinasv/CSBFinder
A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes
Language: Java - Size: 23.2 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 15 - Forks: 3
kiranbandi/mcscanx-synteny-visualizer
A visualization tool for viewing MCscanX Synteny Collinearity files (outdated please check description or readme)
Language: JavaScript - Size: 7.65 MB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2
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: Python - Size: 176 KB - Last synced: 6 months ago - Pushed: almost 2 years ago - Stars: 7 - Forks: 3
jnarayan81/SyntenyParser
Parse the syntney
Language: Perl - Size: 498 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0
