From ec2ca463eac1e1573ced542b4abedcd50441badc Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 24 May 2005 08:51:43 +0000 Subject: [PATCH] added sorting alignments documentation. --- help/help.jhm | 3 ++- help/helpTOC.xml | 1 + help/html/calculations/sorting.html | 41 +++++++++++++++++++++++++++++++++++ 3 files changed, 44 insertions(+), 1 deletion(-) create mode 100755 help/html/calculations/sorting.html diff --git a/help/help.jhm b/help/help.jhm index c843321..4081a57 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -14,7 +14,8 @@ - + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index b60a46c..0bcf3e6 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -30,6 +30,7 @@ + diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html new file mode 100755 index 0000000..c3414bc --- /dev/null +++ b/help/html/calculations/sorting.html @@ -0,0 +1,41 @@ + + +Sorting Sequences + + +

Sorting Sequences

+

Any group of selected sequences may be reordered by pressing the +up or down arrow keys. The whole alignment may also be reordered by +the use of the functions in the Sort menu (Calculate->Sort): +

+
    +
  • Sort by ID +

    Orders the sequences by the alphanumeric (0-9A-Za-z) +precedence of their names.

    +
    • +
  • Sort by Group +

    Places sequences in the same group adjacent to eachother.

    +
    • +
  • Sort by Pairwise Identity +

    Places pairs of sequences together that align with the greatest +fraction of conserved residues. +

    +
    • Sort by Tree Order +

    The leaf ordering of a particular phylogenetic tree is used to +order the sequences corresponding to those leaves in the +alignment.
    +If a tree has been calculated from or associated with the current +alignment, its name will appear in the submenu 'Sort->By Tree Order->'.

    + +

  • Sort by alignment ordering +

    Multiple alignment methods often order the sequences in their +alignments by some measure of sequence identity.
    +If the current alignment has been generated by one of the Jalview +alignment web services, the alignment ordering can be recovered by +its corresponding entry in the 'Sort->By ..' menu. +

    +
    • +
+ + + -- 1.7.10.2