Developed by:
Alberto Riva
DiBiG – ICBR Bioinformatics
University of Florida

FASTools is a collection to command-line tools to manipulate files containing DNA sequences in FASTA and FASTQ format. It offers functions to extract, rename, trim, or filter sequences, to transform them in different ways (reverse-complement, nucleotide substitutions, shuffling, random mutations), to generate random sequences, to perform in-silico restriction enzyme digests or to translate them into amino acid sequences. Additional utilities include generating statistics on the sequences and computing nucleotide frequency distributions. FASTools is optimized to work with very large collections of sequences: sequence files are automatically indexed for faster access.


FASTools is distributed as a GNU/Linux command-line 64bit executable. Source code is available upon request.

Download FASTools

FASTools is also available on HiPerGator, in the dibig_tools module. To use it, execute:

module load dibig_tools


Documentation for FASTools is available in this file.

FASTools provides an integrated help system. Please use

fastools -help Commands

to get a description of all FASTools commands,

fastools -help all

to get a description of all command-line arguments, or

fastools -help option

to get a detailed description of an individual option.