X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fconsensus.html;fp=help%2Fhtml%2Fcalculations%2Fconsensus.html;h=0a0214eedc5d311bf000693830c2b48de282f4ed;hb=c17661b22323a66090ea91e04751aa17461b17c5;hp=ef3e33a4c64223592ddda0560d2ee7ef07cd4186;hpb=a5b213c59c8b5ae9003aca24beb406a9c0aed1ec;p=jalview.git
diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index ef3e33a..0a0214e 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -19,34 +19,50 @@
* along with Jalview. If not, see
Alignment Consensus Annotation
-The consensus displayed below the alignment is the percentage of the modal - residue per column. By default this calculation includes gaps in columns. - You can choose to ignore gaps in the calculation by right clicking on the label - "Consensus" to the left of the consensus bar chart. -
If the modal value is shared by more than 1 residue, a "+" symbol - is used in the display for the simple reason that it is not possible to display - multiple characters in a single character space. -
Copying the consensus sequence
-Select the "Copy Consensus Sequence" entry from -the consensus annotation label to copy the alignment's consensus sequence to the -clipboard. +
+ Alignment Consensus Annotation +
+The consensus displayed below the alignment is the percentage + of the modal residue per column. By default this calculation + includes gaps in columns. You can choose to ignore gaps in the + calculation by right clicking on the label "Consensus" to + the left of the consensus bar chart. +
If the modal value is shared by more than 1 residue, a + "+" symbol is used in the display for the simple reason + that it is not possible to display multiple characters in a single + character space. +
+ Copying the consensus sequence +
++ Select the "Copy Consensus Sequence" + entry from the consensus annotation label to copy the alignment's + consensus sequence to the clipboard. +
+ Sequence logo +
+ By clicking on the label you can also activate the sequence logo. It + indicates the relative amount of residues per column which can be + estimated by its size in the logo. The tooltip of a column gives the + exact numbers for all occurring residues. +Sequence logo
- By clicking on the label you can also activate the sequence logo. It - indicates the relative amount of residues per column which can be - estimated by its size in the logo. The tooltip of a column gives the - exact numbers for all occurring residues. -cDNA Consensus
-A Split Frame View of cDNA and Protein alignments will show the consensus for cDNA below the protein alignment.+ cDNA Consensus +
+ A + Split Frame View of cDNA and + Protein alignments will show the consensus for cDNA below the protein + alignment. +