| 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 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
|
| nthseqset |
Reads and writes (returns) one set of sequences from many
|
| pasteseq |
Insert one sequence into another
|
| revseq |
Reverse and complement a nucleotide sequence
|
| seqret |
Reads and writes (returns) sequences
|
| seqretsetall |
Reads and writes (returns) many sets of 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
|
| splitsource |
Split sequence(s) into original source sequences
|
| 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
|