Synteny Python Packages

pygenomeviz

A genome visualization python package for comparative genomics

jcvi

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

akrup

AKRUP: ancestral karyotype reconstruction universal pipeline

hoodini-colab

Google Colab notebook for running Hoodini gene neighborhood analysis with a nice GUI

synphage

Pipeline to create phage genome synteny graphics from genbank files

daisyblast

Python pipeline for automated synteny block detection and visualization from multiple genomes.

ploidypatch

Duplication-aware, review-first plant gene-model repair with auditable and reversible GFF3 patches

pynteny

Query sequence database by HMMs arranged in predefined synteny structure

phyca

phylogeny and collinearity aware assembly evaluation toolkit.

pyscaf

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

superrec2

Run and compare algorithms for phylogenetic reconciliation and super-reconciliation