<ul>
<li>
<!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
- matrix - C->R should be '3'<br />Old matrix restored with
+ matrix - C->R should be '-3'<br />Old matrix restored with
this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
</li>
<li>
earlier versions of Jalview, gaps matching gaps were
penalised, and gaps matching non-gaps penalised even more.
In the PCA calculation, gaps were actually treated as
- non-gaps - so different costs were applied, which mean't
+ non-gaps - so different costs were applied, which meant
Jalview's PCAs were different to those produced by
SeqSpace.<br />Jalview now treats gaps in the same way as
SeqSpace (ie it scores them as 0). To restore pre-2.10.2