Package: FASTA

FASTA - Pairwise and global similarity searches
Documentation
File format specification	$doc/fasta/format.txt
User's Guide	$doc/fasta/fasta_guide.pdf
Manual	$doc/fasta/fasta36.1.html
User's Guide for FASTA2 programs	$doc/fasta/fasta20.pdf
Web site	https://github.com/wrpearson/fasta36
Data
Platforms: solaris-sparc, linux-intel, solaris-amd64, linux-x86_64, osx-x86_64
Installation: BIRCH
Programs:
align - Pairwise global sequence alignment fasta - Sequence database similarity fastf - compare mixed peptides to a protein database fastm - compare ordered peptides (or short DNA sequences) to a protein or DNA database fasts - compare unordered peptides to a protein database fastx - Database similarity - allow frameshifts between codons fasty - Database similarity - Allow frameshifts within codons fromgb - garnier - Protein secondary structure ggsearch - global alignment of two DNA or protein sequences glsearch - global alignment of DNA or protein query sequence with local alignments of database sequences grease - Protein hydrophobicity lalign - Rigorous local pairwise alignment map_db - read a FASTA (0), GENBANK flat file (1) PIR/VMS (5) or GCG binary (6) sequence database and produce the offsets necessary for efficient memory mapping mrtrans - Align DNA sequences to a protein multiple alignment randseq - Randomize a set of sequences relate - Statistical significance of database similarity ssearch - Rigorous Smith-Waterman database similarity search tfastf - compare mixed peptides to a translated DNA database tfasts - compare unordered peptides to a translated DNA database tfastx - compare a protein to a DNA database, calculating similarities with frameshifts tfasty - compare a protein to a DNA database, calculating similarities with frameshifts