GenomeTools genome analysis system.

A genome visualization python package for comparative genomics

Python programs for processing GFF3 files

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools

Tools for querying and analysis of genomic data

Home of the Genomic Feature and Variation Ontology (GFVO)

A web application for interactive visualization and exploratory data analysis of variant call matrices

Convert sequence IDs between ucsc/refseq/genbank

A Python package for Biopython that gives feature annotations from GenBank records a new and better life

JSON-based FON (Feature Object Notation) format and tools to simplify genomic annotations usage

Genome annotation data analysis and management implemented in pure Python

cool BED-to-GFF3 converter that runs in parallel

Gff-toolbox is a toolbox of commands that enables one to get the gist of their GFF annotation files, as well as to analyse them in different ways.

Plot gene structure

The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome discussion of these recommendations from the larger community.

C# web tool for reading GFF3 files, filtering, ordering, extracting information into Excel, GFF3 files, CDS files, and comparing GFF3 data with FASTA and CDS files.