Functional Analysis of Metagenomes by Likelihood Inference

FASTA is an alignment program for bioinformatics.

FastME provides distance algorithms to infer phylogenies.

Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same squared distance for anchored alignment as other tools.

FastQC is a Quality Control application for FastQ files.

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

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.