<!-- JAL-2549 -->Updated JABAWS client to v2.2
</li>
<li>
- <!-- JAL-2335 -->Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
+ <!-- JAL-2335 -->Filter non-standard amino acids and
+ nucleotides when submitting to AACon and other MSA
+ Analysis services
</li>
<li>
<!-- JAL-2316, -->URLs for viewing database
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><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 />
jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
// for 2.10.1 mode <br />
jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
// to restore 2.10.2 mode <br /> <br /> <em>Note:
these settings will affect all subsequent tree and PCA
- calculations (not recommended)</em>
- </li>
+ calculations (not recommended)</em></li>
<li>
<!-- JAL-2424 -->Fixed off-by-one bug that affected
scaling of branch lengths for trees computed using
doesn't always add secondary structure annotation.
</li>
</ul>
- </div><tr>
+ </div>
+ <tr>
<td width="60" nowrap>
<div align="center">
<strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>