- <li><a name="2102scoremodelbugs"/>
- <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
- and substitution matrix based Tree calculations.<br /> <br />In
- 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 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). <br /> <br />Enter
- the following in the Groovy console to restore pre-2.10.2
- behaviour:<br />
+ <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
+ Jalview's treatment of gaps in PCA and substitution matrix
+ based Tree calculations.<br /> <br />In 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 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). <br /> <br />Enter the following in the
+ Groovy console to restore pre-2.10.2 behaviour:<br />