From e8f8b50cbf08d269bc53a9f51505689ff3674730 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 10 Sep 2015 04:31:38 +0100 Subject: [PATCH] JAL-1645 add reference seq docs to index/etc --- help/help.jhm | 1 + help/helpTOC.xml | 1 + help/html/calculations/referenceseq.html | 50 ++++++++++++++++++++++++++++++ 3 files changed, 52 insertions(+) create mode 100644 help/html/calculations/referenceseq.html 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. +

+ -- 1.7.10.2