and implemented at the SeqSpace server at the EBI. To reproduce
calculations performed with earlier Jalview releases it is necessary
to execute the following Groovy script:
-
<pre>
jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+ jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
</pre>
- Additionally, for PCAs performed with older versions of Jalview and
- the Blosum62 matrix, it is also necessary to import the legacy
- BLOSUM62 score matrix (which is asymmetric for mutations between C to
- R) which can be downloaded at
- http://www.jalview.org/examples/legacyBlosum62.scm
+ This script enables the legacy PCA mode where gaps were treated as
+ 'X', and to modify the BLOSUM62 matrix so it is asymmetric for
+ mutations between C to R (this was a typo in the original Jalview
+ BLOSUM62 matrix which was fixed in 2.10.2).
</p>
-
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