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