The FastX-Toolkit includes FASTQ/A short-reads pre-processing tools.
FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
Funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
FunGAP (Fungal Genome Application Pipline) performs gene prediction on given genome assembly and RNA-seq reads.
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.
Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training.