Funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).

GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion.

The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers.

GDC is a data transfer tool used for accessing National Cancer Institute data.

Gene Model Mapper (GeMoMa) is a homology-based gene prediction program.

Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training.

GenomeTools is versatile open source genome analysis software.

GSNAP: Genomic Short-read Nucleotide Alignment Program