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

A genome visualization python package for comparative genomics

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

CoGe (Comparative Genomics) Platform

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

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, dire…

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

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

A shiny application to visualize MCscan result

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

Synteny Mapping and Analysis Program

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

Pipelines for the production of Treeval data

AccuSyn: An Accurate Web-based Genome Synteny Browser

Finding regions of similarity between plasmids

Query sequence database by HMMs arranged in predefined synteny structure

Wrapper for the genoPlotR R package. This wrapper makes phylogeny, genbank files and blast comparisons that is needed for the genoPLotR package

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

Trace intervals between genomes using a synteny map

Pipeline to create phage genome synteny graphics from genbank files