From Bioinformatics.Org Wiki
- consed - A Unix-based Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
- phrap - a program for assembling shotgun DNA sequence data
- sp2fasta - produce a file in FASTA format from one in SWISSPROTor EMBL flat file format
- Staden Package - This is a free to academics (charge for commercial users) package including sequence assemble, trace viewing/editing and sequence analysis tools. It also includes a GUI to the free EMBOSS suite.