source: trunk/HELP_SOURCE/source/merge_species.hlp

Last change on this file was 19532, checked in by westram, 3 months ago
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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           Merge Similar Species
12
13OCCURRENCE      ARB_NT/Species/Merge Species/Create merged species from similar species
14                ARB_NT/Sequence/Concatenate sequences/MERGE SIMILAR SPECIES
15
16DESCRIPTION
17
18            "Merge Similar Species" creates new species by merging
19            fields and alignments of several similar species.
20
21            - Mark all species that should be examined for similarity.
22
23            - Select a database field entry by clicking on the first
24              button to set a similarity-criterion used to detect
25              candidates for merging (for e.g., full_name).
26
27            - Specify the new field name to which the "number of merged
28              species" information is to be stored (e.g., merged_species).
29
30            - Press "Merge similar species ..." to start.
31
32SECTION     Merge and concatenate
33
34            From LINK{concatenate.hlp} you can access a special flavor of the
35            "Merge similar species" function, that will also concatenate the
36            selected alignments.
37
38            That version is useful after merging species of two (or more) independent
39            databases, that contain different genes of the same organisms.
40
41            After merging you'll end up with data like:
42
43                  name           "SpecExe1"
44                  full_name      "Species exemplares"
45                  ali_5s/data    "--AC--GU--"
46
47                  name           "SpecAlt1"
48                  full_name      "Species alternatio"
49                  ali_5s/data    "--AU-GGC--"
50
51                  name           "SpecExe2"
52                  full_name      "Species exemplares"
53                  ali_16s/data   "----U-A---G-C-----"
54
55                  name           "SpecAlt2"
56                  full_name      "Species alternatio"
57                  ali_16s/data   "----G-A---UUC-----"
58
59
60            Using merge and concatenate with 'full_name' as similarity criterion,
61            you can generate data like
62
63                  name                 "SpecExe3"
64                  full_name            "Species exemplares"
65                  ali_5s_and_16s/data   "--AC--GU--XXX----U-A---G-C-----"
66
67                  name                 "SpecAlt3"
68                  full_name            "Species alternatio"
69                  ali_5s_and_16s/data   "--AU-GGC--XXX----G-A---UUC-----"
70
71
72NOTES           There's a second (older) function to merge species: see LINK{species_join.hlp}
73
74EXAMPLES        None
75
76WARNINGS        None
77
78BUGS            No bugs known
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