From 45b21046f407e78f92b496083ffeff13a4790b2b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 16 Oct 2018 17:22:46 +0100 Subject: [PATCH] JAL-3127 updated colours menu and tree view documentation --- help/html/calculations/treeviewer.html | 13 ++++++++----- help/html/menus/alignmentMenu.html | 8 +++++++- help/html/menus/alwcolour.html | 5 +++++ 3 files changed, 20 insertions(+), 6 deletions(-) diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index 3d6245e..8cb2b59 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -36,20 +36,20 @@

Selecting Sequence Leaf Nodes
- Selecting sequence ids at the leaves of the tree selects the + Selecting sequence IDs at the leaves of the tree selects the corresponding sequences in the original alignment. These selections are also reflected in any other analysis windows associated with the alignment, such as another tree viewer.

- Grouping sequences by partitioning the - tree at a particular distanec
Clicking anywhere along + Grouping sequences by partitioning the + tree at a particular distance
Clicking anywhere along the extent of the tree (but not on a leaf or internal node) defines a tree 'partition', by cutting every branch of the tree spanning the depth where the mouse-click occurred. Groups are created containing sequences at the leaves of each connected sub tree. These groups are each given a different colour, which are reflected in other windows - in the same way as if the sequence ids were selected, and can be + in the same way as if the sequence IDs were selected, and can be edited in the same way as user defined sequence groups.

@@ -58,7 +58,10 @@ identifying specific patterns of conservation and mutation corresponding to the overall phylogenetic structure, when combined with the conservation - based colour scheme. + based colour scheme.To distinguish parts of the alignment assigned + to different groups, you may also enable the Sequence ID colour + scheme via the Alignment + window's Colours menu (Since 2.11).

Selecting Subtrees and changing the branch diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index f3ab75d..3a057a8 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -483,7 +483,13 @@ See colours for a description of all colour schemes.
-

  • By Conservation
    +
  • Sequence ID
    Shades + sequences using their Sequence ID colour. Useful when + performing tree + based subfamily analysis. +
    • +
  • By Conservation
    See Colouring by Conservation.
    • diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html index e62a130..9a96595 100755 --- a/help/html/menus/alwcolour.html +++ b/help/html/menus/alwcolour.html @@ -45,6 +45,11 @@ a description of all colour schemes.
    +
  • Sequence ID
    Shades + sequences using their Sequence ID colour. Useful when performing + tree + based subfamily analysis. +
  • By Conservation
    See Colouring by Conservation. -- 1.7.10.2