The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or SHMR) service (Brandt, Feenstra and Heringa, 2010) available from the Analysis sub-menu of the alignment window's web services menu provides a method for the identification of significant patterns of sub-family variation amongst the columns of an alignment.

Instructions for use
The service requires a protein sequence multiple alignment that has been sub-divided into groups containing at least two non-identical protein sequences. An easy way to create groups is to use the built-in neighbour-joining or UPGMA tree routines to calculate a tree for the alignment, and then click on the tree to subdivide the alignment.

The SHMR service operates on the currently selected visible region(s) of the alignment. Once submitted, a job progress window will display status information about your job, including a URL which allows you to visit the status page on the IBIVU SHMR server.

When the job is complete, Jalview will automatically open a new window containing the alignment and groups that were submitted for analysis, with additional histograms added portraying the SHMR scores for each column of the sub-grouped alignment.

If you use this service in your work, please cite :
Brandt, B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting functional specificity from sequence alignment. Nucleic Acids Res. 38: W35-W40. (* joint first authors)

Note: The Multi-Harmony service is implemented with a prototype of Jalview's RESTful web service client introduced in Jalview 2.7. A few bugs remain in this prototype, which we intend to fixed in version 2.7.1.