| Cbstools | The CBSTOOLS package is a set of wrappers to selected applications from the CBS group in Denmark. |
| Domainatrix | The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. |
| Domalign | The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. |
| Domsearch | The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. |
| Emnu | The EMNU package is a simple EMBOSS menu system written by Gary Williams at HGMP. |
| Esim4 | The ESIM4 package is an EMBOSS conversion of the SIM4 package from Liliana Florea. |
| Hmmernew | EMBASSY HMMERNEW is a suite of application wrappers to the original hmmer v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be installed on the same system as EMBOSS and the location of the hmmer executables must be defined in your path for EMBASSY HMMER to work. |
| Iprscan | The IPRSCAN package is a wrapper for the interproscan program. |
| Memenew | The EMBASSY MEME package contains 'wrapper' applications providing an EMBOSS-style interface to the applications in the original MEME package version 4.0.0 developed by Timothy L. Bailey. |
| Mira | The MIRA package is a fragment assembly program from Bastien Chevreux. The program was converted to EMBOSS by Alan Bleasby as two applications, one for EST assembly and one for shotgun fragment assembly |
| Mse | The MSE package is a multiple sequence editor. The program was contributed to the EMBOSS package by the author, Will Gilbert, as one of the first EMBASSY programs. |
| Myembossdemo | The MYEMBOSSDEMO package contains example applications using EMBOSS data types |
| Phylipnew | The PHYLIPNEW programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, version 3.69. |
| Signature | The SIGNATURE programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. |
| Structure | The STRUCTURE programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. |
| Topo | The TOPO package is a graphics program to display membrane protein topology by Susan Jean Johns. |
| Vienna | These programs are adapted from the VIENNA RNA package. |