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If you use any of the scripts in this repositoy please cite it as follows:

Parker, D. J. (2016). fasta_tools. Zenodo.

NOTE: help messages can be displayed for all scripts by running them without any arguments provided (i.e. python [name of script]) or specifying -h (python [name of script] -h) . All scripts written in python3.4 or higher.

generic scripts

Some basic scripts for commonly performed tasks on fasta files.

  • | extract fasta seqs specified by name (or select all but those specified (invert option))
  • | unwrap a wrapped fasta file
  • fasta_select_by_len | select seqs of specified length (less-than, greater-than, or range)
  • | calc min, min length, max length, mean length, N50, and base comp of fasta sequences
  • | get len of all seqs


  • | takes a fasta alignments as input, and outputs 3 fasta alignments each a different position (1,2,3)
  • takes a number of separate fasta file alignments as input, and concats them
  • This program takes an alignment file as input It trims alignments to remove regions with gaps in two main ways it trims gaps from the ends of the alignment it trims gaps from inside the alignment iteratively, starting with the closest to the end of the alignment (greater than minimum gapsize), until no gaps larger than minimum gapsize")