source: tags/ms_r16q4/HELP_SOURCE/oldhelp/dist.hlp

Last change on this file was 14622, checked in by westram, 8 years ago
  • reintegrates 'ui' into 'trunk'
    • implements #656
    • adds instant update for
      • next neighbour search
      • branch analysis (mark functions)
      • arb-phylo (filter setup)
  • adds: log:branches/ui@14588:14621
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 7.7 KB
Line 
1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      mark.hlp
5UP      phylo.hlp
6
7#Please insert subtopic references  (line starts with keyword SUB)
8SUB     user_matrix.hlp
9SUB     savedef.hlp
10SUB     props_frame.hlp
11SUB     sel_fil.hlp
12SUB     awt_csp.hlp
13SUB     bootstrap.hlp
14
15
16# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
17
18#************* Title of helpfile !! and start of real helpfile ********
19TITLE           Neighbour joining
20
21OCCURRENCE      ARB_NT/Tree/Build tree from sequence data/Distance matrix methods/Distance matrix + ARB NJ
22
23DESCRIPTION     Reconstructs a tree for all or marked species by first
24                calculating binary distances and subsequently applying the
25                neighbour joining method.
26
27                The tree topology is stored in the database and can be displayed
28                within the tree display area of the 'ARB_NT' window.
29
30                1. Mark all interesting species.
31
32                2. Select all or marked species from the 'Select Species' menu
33                   of the 'NEIGHBOUR JOINING' window.
34
35                3. Select Alignment from the 'Select Alignment' subwindow of
36                   the 'NEIGHBOUR JOINING' window.
37
38                4. Display the 'Select Filter' window by pressing the button
39                   after the 'Filter' prompt and define an alignment-associated
40                   mask which defines alignment positions to include for treeing.
41
42                5. Define Weights: @@@ not implemented
43
44                6. Select rate matrix (only implemented for some corrections; see LINK{user_matrix.hlp})
45
46                7. Type characters for the exclusion of alignment postions to
47                   the 'Exclude Column' subwindow. The positions are
48                   excluded from the calculation of binary distance values
49                   if one of the specified characters is present in one or
50                   both sequences. The described function acts as a second
51                   filter and affects only the particular sequence
52                   pairs, not the whole alignment.
53
54                8. Select the type of distance correction from the 'Distance
55                   Correction' submenu. You can use the program to detect
56                   the best correction for you by pressing the AUTODETECT
57                   button.
58
59                   none:
60
61                        Differences/Sequence length. May be a good
62                        choice for short sequences (length < 300).
63
64                   similarity:
65
66                        1.0 - Differences/Sequence_Length
67
68                   jukes-cantor:
69
70                        Accounts for multiple base changes, assumes
71                        equal base frequencies.
72                        Good choice for medium sized sequences
73                        ( 300 - 1000/2000 sequence length )
74
75                   felsenstein:
76
77                        Similar to jukes-cantor transformation. Allows
78                        unequal base frequencies.
79                        ( length > 1000/2000 )
80
81                   olsen:
82
83                        As Felsenstein, except the base frequencies are
84                        calculated for each pair of sequences.
85
86                   from selected tree:
87
88                        This is NOT a distance correction! By selecting 'from selected tree'
89                        distances are not calculated using sequence data.
90                        Instead they are extracted from the
91                        tree currently selected in the 'Trees in Database' selection list.
92
93                        The distance between two species is defined as the sum of the lengths
94                        of all branches that connect these two species.
95
96                        Please note that this is an experimental feature. The distances between two species
97                        are not directly based on the sequence differences between these two species.
98                        Instead they reflect the evolutionary distance assumed by the tree reconstruction
99                        algorithm used to build the tree.
100
101                        The distances extracted from a tree are expected to be (slightly) bigger than
102                        the distances directly calculated from the sequences.
103                        This seems reasonable, because it is very unlikely, that evolution always took the
104                        shortest possible way (which is represented by the direct sequence distance).
105                        This effect increases for more distant (unrelated) species, reflecting the
106                        indirections evolution most likely made.
107
108                   Please note:
109
110                          the other correcting functions are in an experimental state.
111                          Wait for new release.!!!
112
113                9. Select a name for the tree from the 'Trees in Database'
114                   subwindow or type a new tree name.
115                   The tree name has to be 'tree_*'.
116                   An existing tree with that name will be deleted.
117
118                10. Press the 'CALCULATE TREE' button
119
120                11. Now you may display the new tree in the ARB_NT main window
121                        by selecting its name from the <Tree/Select> subwindow.
122                        If its name is already selected, you will not need to
123                        reselect it.
124
125                The distance matrix can be written to an ascii file:
126
127                        Press the <SAVE MATRIX> button to display the 'SAVE
128                        MATRIX' window. Select a file from the 'Directories
129                        and Files' subwindow or type a file name to the 'FILE
130                        NAME' subwindow. Press the <SAVE> button.
131                        The suffix displayed in the 'SUFFIX' subwindow is added
132                        to the typed file name and defines the selection of
133                        files listed in the 'Directories and Files' subwindow.
134
135SECTION         Calculate compressed matrix
136
137                You may select a tree to calculate a compressed matrix. A
138                compressed matrix contains columns for all folded groups
139                visible in the displayed tree (i.e. not for unfolded groups
140                and not for folded groups inside other folded groups).
141               
142                Species inside such groups are NOT listed as single entries.
143               
144                The distance shown for each group is the arithmetic average of
145                of the distances of all contained species.
146
147SECTION         Automatic calculation
148
149                There are two toggles in the ARB_DIST main window allowing to
150                trigger instant recalculation:
151
152                - 'Auto recalculate' will force recalculation of the matrix
153                - 'Auto calculate tree' will force calculation of the tree
154
155                If 'Auto calculate tree' is checked, the tree will be calculated
156                whenever the matrix has been updated.
157
158                If 'Auto recalculate' is checked, the matrix will be recalculated
159                whenever any input changes, e.g. if
160
161                - the filter is changed (or its underlaying SAI changes),
162                - the excluded columns change,
163                - the user defined matrix changes,
164                - the correction is changed,
165                - the sequence data changes or species marks change or
166                - the tree selected for compression or sorting changes or a different
167                  tree is selected.
168
169                As you might have guessed, this is only useful for smaller sets of sequences.
170
171                Some suggestions:
172
173                     You might for example display the resulting NJ tree in one window and
174                     play with distance parameter to instantly see their effect on the tree.
175
176                     Or you may unmark unwanted species/subtrees in the tree display.
177
178                     Or you might align sequences to see the effect on the resulting topology.
179
180
181NOTES           Computing time can be estimated using the following formula:
182
183                        time = (Sequence_Length * Nr.of.Spec * Nr.of.Spec)/
184                                Computer Power
185
186                                Example: Sparc 10, 74 Sequences, length 8000 characters
187                                         -> 10 Seconds
188
189
190WARNINGS        Don't try to build a tree with the 'similarity' distance
191                correction selected.
192
193                Distance values calculated without distance correction are strictly inside range [0.0 .. 1.0].
194                Same is true for 'similarity' distance "correction".
195                With distance corrections, the range does vary depending on the correction method.
196
197BUGS            None
198
Note: See TracBrowser for help on using the repository browser.