X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fquality.html;h=cab1ea85773a80645c236b6bfe5b2b1d6b5a2d5d;hb=b4b901505310c3bdd1809f122abed6799c2fa664;hp=28841b2b6b403eeee4384008d1392f88cf274b04;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git
diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html
index 28841b2..cab1ea8 100755
--- a/help/html/calculations/quality.html
+++ b/help/html/calculations/quality.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Alignment Quality Annotation
@@ -27,7 +30,7 @@ measure of the likelihood of observing the mutations (if any) in a particular column of the alignment.More precisely, the quality score is inversely proportional to the -average cost of all pairs of mutations oberved in a particular column +average cost of all pairs of mutations observed in a particular column of the alignment - a high alignment quality score for a column would suggest that there are no mutations, or most mutations observed are favourable. @@ -36,8 +39,8 @@ favourable.
The Algorithm
The quality score is calculated for each column in an alignment by
summing, for all mutations, the ratio of the two BLOSUM 62 scores for
-a mutation pair and each residue's conservered BLOSUM62 score (which
-is higher). This valueis normalised for each column, and then plotted
+a mutation pair and each residue's conserved BLOSUM62 score (which
+is higher). This value is normalised for each column, and then plotted
on a scale from 0 to 1.