+ Alignment Conservation Annotation +
+
+ This is an automatically calculated quantitative alignment
+ annotation which measures the number of conserved physico-chemical
+ properties conserved for each column of the alignment. Its
+ calculation is based on the one used in the AMAS method of multiple
+ sequence alignment analysis :
+
+ Conservation is measured as a numerical index reflecting the + conservation of physico-chemical + properties in the alignment: Identities score highest, and the + next most conserved group contain substitutions to amino acids lying + in the same physico-chemical class. +
+Conservation is visualised on the alignment or a sequence group + as a histogram giving the score for each column. Conserved columns + are indicated by '*' (score of 11 with default amino acid property + grouping), and columns with mutations where all properties are + conserved are marked with a '+' (score of 10, indicating all + properties are conserved).
++ Mousing over a conservation histogram reveals a tooltip which + contains a series of symbols corresponding to the physicochemical + properties that are conserved amongst the amino acids observed at + each position. In these tooltips, the presence of ! implies + that the lack of a particular physicochemical property is conserved + (e.g. !proline). +
+
+ Colouring an alignment by conservation
+ Conservation scores can be used to colour an alignment. This is
+ explained further in the help page for conservation
+ colouring.
+
+ Group conservation
If sequence groups have
+ been defined, then selecting option 'Group Conservation' in the Annotations menu will
+ result in Conservation being calculated for each group, as well as
+ the alignment as a whole.
+