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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
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5#Please insert subtopic references  (line starts with keyword SUB)
6#SUB    subtopic.hlp
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8# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
9#
10# ----------------------------------------------------------------------       ***********************
11# @@@ this page is predecessor of phylo.hlp and dist.hlp
12# @@@ Please eliminate it and remove all references!
13# ----------------------------------------------------------------------       ***********************
14
15#************* Title of helpfile !! and start of real helpfile ********
16TITLE           Matrices, Masks, Profiles V1.0
17
18OCCURRENCE      ARB_NT/Tree/Dist Matrix V 1.0
19
20DESCRIPTION     This tool allows to calculate distance and similarity matrices
21                for the marked species. Conservation profiles can be established
22                and used as filters for column selection by other programs.
23
24                1. Selection of columns:
25
26                Select part of the alignment to analyze by typing first and last
27                        column numbers after the 'start at column:' and 'stop at
28                        column:' prompts, respectively, and press 'Return' on
29                        the keyboard.
30
31                Select minimum and maximum similarities for the individual
32                        columns to be included for similarity or distance matrix
33                        calculation by typing the values (50 means the most
34                        frequent base at a particular position is shared by at
35                        least 50% of all marked sequences (species)) after the
36                        'minimum similarity:' and 'maximum similarity:' prompts,
37                        respectively, and press 'Return' on the keyboard.
38
39                Define whether alignment gaps and ambiguities within individual
40                        marked sequences (species) should be taken into account:
41
42                        Use the right mouse button to display the submenus
43                        associated to the items below the 'markerline:' prompt
44                        by pressing the respective buttons.
45
46                                don't count:
47                                        Calculate conservation from unambiguous
48                                        bases only
49
50                                don't use column if maximal:
51                                        Exclude column if the respective symbol
52                                        is present in the majority of the marked
53                                        sequences.
54
55                                exclude column:
56                                        Exclude column if the respective symbol
57                                        is present in any of the marked
58                                        sequences.
59
60                                treat as ambiguous:
61                                        Take the respective symbol as an
62                                        unambiguous residue.
63
64                2. After selecting columns define how to treat ambiguities for
65                        distance calculations:
66
67                        Use the right mouse button to display the submenus
68                        associated to the items below the 'distance matrix:'
69                        prompt by pressing the respective buttons.
70
71                                don't count:
72                                        The particular position is not
73                                        included for binary distance
74                                        calculations if the symbol is
75                                        present in one or both sequences.
76
77                                use distance table:
78                                        the symbols are treated as unambiguous
79                                        residues
80
81                3. Calculate profiles and matrices:
82
83                        Use the right mouse button to display the 'CALCULATE'
84                        menu and select 'markerline' (profile) or 'distance
85                        matrix' by releasing the mouse button while the cursor
86                        is positioned on the respective menu button.
87
88                4. Display results:
89
90                        Use the right mouse button to display the 'VIEW'
91                        menu and select 'species', 'markerline' or 'distance
92                        matrix' by releasing the mouse button while the cursor
93                        is positioned on the respective menu button. The names,
94                        the aligment of the marked sequences and the
95                        conservation profile, or the distance matrix are shown
96                        within the display area, respectively.
97
98                        The profile:
99
100                        The fraction of sequences sharing most frequent residue
101                        at a particular alignment position is shown as a number
102                        to read bottom down. Alternatively, the profile can be
103                        displayed as a curve by pressing the <toggle> button in
104                        the left part of the window. It can be smoothed by
105                        selecting a number from the 'smooth' menu (left part of
106                        the window).
107
108                        Editing the aligned sequences and profiles, a name can
109                        be selected by moving the cursor to it and pressing the
110                        left mouse button. Pressing the <reference> button, the
111                        respective sequence is used as a filter superimposed to
112                        profile. This allows to exclude further positions from
113                        subsequent calculations which are not occupied by bases
114                        in the reference.
115
116                        Tha matrix:
117
118                        Editing the matrix, mean values can be calculated for
119                        groups of organisms displayed as triangles (radial tree)
120                        or rectangles (dendrogram) in a tree stored in the
121                        database. The grouping currently or most recently
122                        displayed is used for selecting sequences for the
123                        calculation of mean values. Select a tree by pressing
124                        the <grouping> button in the left area of the window.
125
126                5. Save results:
127
128                        To export distances and profiles (not graphs!!) to
129                        ascii files, use the right mouse button to display the
130                        'SAVE' menu and select the corresponding menu item by
131                        releasing the mouse button while the cursor is
132                        positioned on it.
133
134                                uncoded mline:
135                                        The positional conservation is encoded
136                                        by a sequence of letters: A = 1%,
137                                        B = 5%, ...., Z = 100%.
138
139                                bin mline:
140                                        Included and excluded columns are
141                                        indicated by 1 and 0, respectively.
142
143                                % dif. matrix:
144                                        Dissimilarity values.
145
146                                % sim. matrix:
147                                        Similarity values.
148
149                                phyl/prot distmat:
150                                        Corrected distances according Jukes and
151                                        Cantor (nucleic acid sequences only).
152
153                                pos. vari:
154                                        Number of different residues at the
155                                        particular alignment position.
156
157                6. Reconstruct a tree:
158
159                        Press the <NEIGHBOR> button. The tree is reconstructed
160                        using the neighbour joining method and is stored in the
161                        database as 'tree_neighbour'.
162
163                7. Store profile in the database:
164
165                        Press the <ARBSAVE> button to store any calculated
166                        profile 0 / 1 encoded in the database (SAI). The profile
167                        can be used as filter for other ARB tools.                             
168                         
169NOTES           A new version of the tool is under development.
170
171                It is recommended to calculate profiles here, to save them in
172                the database, and to reconstruct distance matrix trees using
173                'ARB_NT/Tree/Neighbour joining' in combination with the profile
174                as filter.
175
176EXAMPLES        None
177
178WARNINGS        Whenever text is typed to the window, press 'Return' on the
179                keyboard, to ensure that the information is recognized by the
180                program!!!
181
182BUGS            No bugs known
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