X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwcalculate.html;h=50bb37b0f6489f22a53c546140298110c3cb56af;hb=830a19575c85366f00f6025f9fe98ef8298fc289;hp=28ff3d6d393475a230b4bcf6c3922d446cc9964e;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 28ff3d6..50bb37b 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -1,21 +1,24 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Alignment Window Menus @@ -79,7 +82,15 @@ 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.
- +
  • Translate as cDNA (not applet)
    This option is visible for nucleotide alignments. + Selecting this option shows the DNA's calculated protein product in a new window. Note that the + translation is not frame- or intron-aware; it simply translates all codons in each sequence, using the + standard genetic code (any incomplete final codon is discarded). + You can perform this action on the whole alignment, + or selected rows, columns, or regions.
    • +
  • Get Cross-References (not applet)
    This option is visible where sequences have cross-references to + other standard databases; for example, an EMBL entry may have cross-references to one or more UNIPROT entries. + Select the database to view all cross-referenced sequences in a new window.
  • Autocalculate Consensus
    For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy