Program name	Description
aligncopy	Reads and writes alignments
aligncopypair	Reads and writes pairs from alignments
biosed	Replace or delete sequence sections
codcopy	Copy and reformat a codon usage table
cutseq	Removes a section from a sequence
degapseq	Removes non-alphabetic (e.g. gap) characters from sequences
descseq	Alter the name or description of a sequence
entret	Retrieves sequence entries from flatfile databases and files
extractalign	Extract regions from a sequence alignment
extractfeat	Extract features from sequence(s)
extractseq	Extract regions from a sequence
featcopy	Reads and writes a feature table
featreport	Reads and writes a feature table
listor	Write a list file of the logical OR of two sets of sequences
makenucseq	Create random nucleotide sequences
makeprotseq	Create random protein sequences
maskambignuc	Masks all ambiguity characters in nucleotide sequences with N
maskambigprot	Masks all ambiguity characters in protein sequences with X
maskfeat	Write a sequence with masked features
maskseq	Write a sequence with masked regions
newseq	Create a sequence file from a typed-in sequence
nohtml	Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn	Remove carriage return from ASCII files
nospace	Remove all whitespace from an ASCII text file
notab	Replace tabs with spaces in an ASCII text file
notseq	Write to file a subset of an input stream of sequences
nthseq	Write to file a single sequence from an input stream of sequences
pasteseq	Insert one sequence into another
revseq	Reverse and complement a nucleotide sequence
seqret	Reads and writes (returns) sequences
seqretsplit	Reads sequences and writes them to individual files
sizeseq	Sort sequences by size
skipredundant	Remove redundant sequences from an input set
skipseq	Reads and writes (returns) sequences, skipping first few
splitter	Split sequence(s) into smaller sequences
trimest	Remove poly-A tails from nucleotide sequences
trimseq	Remove unwanted characters from start and end of sequence(s)
trimspace	Remove extra whitespace from an ASCII text file
union	Concatenate multiple sequences into a single sequence
vectorstrip	Removes vectors from the ends of nucleotide sequence(s)
yank	Add a sequence reference (a full USA) to a list file