To incorporate third party applications into EMBOSS takes significant work, regardless of whether an application is wrapped or ported. This work is very worthwhile though because of benefits in terms of distribution (the software will reach more users) and, in some cases, because of lowered costs of training, support and maintenance. Moreover, any incorporated software can make use of inbuilt EMBOSS functionality such as support for common sequence formats and will be integrated into the many available EMBOSS interfaces. These include graphical user interfaces, workflow software and web services.

Fully ported software provides the most flexibility but this comes at a high relative maintenance cost. Nonetheless, this is the preferred route where the code is to be essentially adopted by EMBOSS. More or less the same flexibility can be achieved in a wrapper by the use of temporary files, although there are drawbacks and potential complications to this. For example, code for interconverting file formats is needed.