X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=eae9c92490347f8b7ee758a4030ec572a61e531e;hb=2b3bd506ee1cc2d1a26a3425ccba48665179a9fb;hp=9d40868b3c59e930f4c9e8701fbb8405ffdb3a92;hpb=5a6d8d69732445af2189fc4bab7a09dbd77bb829;p=jalview.git diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 9d40868..eae9c92 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -1,4 +1,21 @@ + Alignment Window Menus @@ -9,6 +26,9 @@
  • by ID
    This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted.
    • +
  • by Length
    + This will sort the sequences according to their length (excluding gap characters). If the sort is + repeated, the order of the sorted sequences will be inverted.
  • by Group
    This will sort the sequences according to sequence name. If the sort is repeated, the order of the sorted sequences will be inverted. @@ -18,7 +38,8 @@ identity to the consensus sequence. The most similar sequence is put at the top.
  • The Sort menu will have - some additional options if you have just done a multiple alignment calculation, + some additional options if the alignment has any associated + score annotation, or you have just done a multiple alignment calculation or opened a tree viewer window.
    • @@ -44,6 +65,12 @@ in the alignment. See Principal Component Analysis.
    +
  • Extract Scores ... (optional)
    + This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.
    + When selected, these numbers are parsed into sequence associated annotation which can + then be used to sort the alignment via the Sort by→Score menu.
    +
    • +
  • Autocalculate Consensus
    For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations