Gff3 Python Packages

pygenomeviz

A genome visualization python package for comparative genomics

filterx

process any file in tabular format. Fasta/fastq/GTF/GFF/VCF/SAM/BED

gff3tool

Python programs for processing GFF3 files

tigre

TIGRE is a Python CLI for large scale extraction of intergenic regions.

divbrowse

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

bioino

💻 Interconverting FASTA, GFF, and CSV.

gdt

GDT is a tool for gene dictionary management, works with annotated genomes, handles .gdict and GFF3 files, and provides both programmatic and interactive interface.

vcfsynonymous

read VCF and select synonymous or non-synonymous coding variants

genome-format-converters

A unified Python CLI for 30 bioinformatics file-format conversions (VCF, GFF3, GTF, BED, GenBank, FASTA, FASTQ, BAM, EIGENSTRAT, PLINK, MAF, MUMmer, HMMER, Newick) with consistent flags, batch mode, and a published Stage 1 benchmark vs convertf, plink2, AGAT, gffread, UCSC, EMBOSS, pyhmmer.

ploidypatch

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

gff-toolkit

tools for handling gff files

gff2parquet

Utility CLI for handling GFF files (incl. converting to parquet)

gffy

gffy — A fast GFF statistics extractor. Well, because the world needed another one.

gbgb

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