source: branches/lib/HELP_SOURCE/source/multifurcate.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
File size: 4.1 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Multifurcate tree
12
13OCCURRENCE      ARB_NT/Tree/Modify branches/Multifurcate
14
15DESCRIPTION     Trees constructed by treeing algorithms often suggest a precision
16                which does in fact not exist in reality. To make it impossible to draw wrong
17                conclusions from your tree, you might consider to multifurcate specific
18                branches, especially such with low bootstrap values.
19
20                In the 'Multifurcate tree' window you can restrict which branches shall be
21                multifurcated by specifying lower limits for
22                  * bootstrap and/or
23                  * branchlength.
24
25                All branches below the specified and selected limits will be multifurcated,
26                i.e. their length will be set to zero and their bootstrap value (if any) will be
27                removed by clicking on the 'Multifurcate' button.
28
29                This is only applied to terminal (i.e. leaf) branches, if 'Also apply to
30                terminal branches' is checked.
31
32                The algorithm does not change the sum of the branchlengths of the tree (which is
33                a measure for the phylogenetic distance between all tree members).
34                To achieve that the algorithm distributes the former branchlength of each removed
35                branch to its directly adjacent neighbour branches.
36
37                Removing the branch C from this example tree
38
39                            B
40                         +----
41                      A  |
42                     ----+       D
43                         |    +----
44                         +----|
45                            C +----
46                                 E
47
48                will result in a multifurcated tree
49
50                             b
51                          +-----
52                      a   |
53                     -----+  d
54                          +-----
55                          |
56                          +-----
57                             e
58
59
60                with modified branchlengths, where
61
62                     SUM(a,b,d,e) = SUM(A,B,C,D,E)
63
64                The distribution is performed proportionally to the length of the target branches
65                of the distribution, i.e. longer branches receive more of the distributed
66                length than shorter branches.
67
68                Branches with zero branchlength are never changed, as they already represent (and
69                will remain) multifurcations. Instead the length is distributed to the next
70                adjacent branches beyond the multifurcation. This is true for existing and for
71                just created multifurcations.
72
73                The distribution simultaneously takes place at all affected branches,
74                always considering the former branchlengths for calculating the proportion
75                and avoiding summarizing effects at repeatedly affected branches (i.e. at branches
76                with multiple removed neighbour branches)
77
78NOTES           The sum of all branchlengths in a tree modified with 'Multifurcate tree' will
79                remain constant (disregarding possible numerical problems and the abnormal case that
80                ALL branches get multifurcated).
81
82                See LINK{branch_analysis.hlp} on HOWTO calculate the sum of all
83                branchlengths of a tree.
84
85EXAMPLES        To see how the distribution works for single branches, display a small tree
86                with only a few species, select the MULTIFURCATE MODE (see LINK{mode_length.hlp})
87                and drag some branches to scale their length.
88
89WARNINGS        Selecting none of the limits will remove the lengths from all branches and the sum
90                of branchlengths of the tree will change to zero. This
91                option makes no sense at all and is only provided for your relief in case you're
92                fed up with topologies and feel the urgent need to easily get rid of one of them.
93
94BUGS            No bugs known
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