From: Jim Procter Date: Thu, 10 Sep 2015 03:31:38 +0000 (+0100) Subject: JAL-1645 add reference seq docs to index/etc X-Git-Tag: Release_2_10_0~434 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e8f8b50cbf08d269bc53a9f51505689ff3674730;p=jalview.git JAL-1645 add reference seq docs to index/etc --- diff --git a/help/help.jhm b/help/help.jhm index 221a8a7..ce98085 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -81,6 +81,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index b956004..9ae45b9 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -114,6 +114,7 @@ + diff --git a/help/html/calculations/referenceseq.html b/help/html/calculations/referenceseq.html new file mode 100644 index 0000000..27d2cd2 --- /dev/null +++ b/help/html/calculations/referenceseq.html @@ -0,0 +1,50 @@ + + + +Reference Sequences + + +

+ Reference Sequence Alignment Views +

+

+ The reference sequence for an alignment is indicated by its ID being + shown in bold. When a reference sequence has been defined, the Format→Show + unconserved option highlights mutations with respect to the + reference sequence, rather than the alignment's consensus sequence. +

+

+

    +
  • Jalview automatically assigns a reference sequence when JPred4 predictions are + imported. +
    • +
  • Assigning a reference sequence
    A + sequence can be marked as the reference sequence by right-clicking + on it's ID to open the popup menu, and selecting the "(Sequence + ID)→Mark as Reference" entry."
    • +
+

+ Reference sequence based alignment visualisation was + introduced in Jalview 2.9. +

+