FASTA is an alignment program for bioinformatics.
fastGEAR is software for analysing sequence alignments.
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.
fastStructure is an algorithm for inferring population structure from large SNP genotype data.
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.