fasta-tools: Simple programs to manipulate fasta files

For all programs:

Run with -h for usage

Program descriptions:

fasta_seq_lens.sh

Get lengths of all sequences in a fasta file

fasta_single_line.sh

Convert fasta file to have each sequence on a single line (not including header)

fasta_seq_extractor.pl

Extract entire sequences whose names match a regular expression and/or list of sequence headers

fasta_region_extractor.pl

Extract a given region from a given sequence in a fasta file

pairwise_align_bed_regions.py

Perform pairwise alignments between sequences extracted from a fasta file using BED records

pairwise_alignment.py

Perform a pairwise global alignment between two sequences in a fasta file