Readseq is a classic, dating from 1989. Developed by Don Gilbert, this program reads and writes nucleotide and protein sequences in many useful formats. The Java version is the most current; we're using Version 2.
To run Readseq use:
java -cp readseq.jar run options inputfiles
For more details use:
java -cp readseq.jar help more
This chapter contains a list of the command line options used in Readseq.