Matrices, Masks, Profiles V1.0OCCURRENCE
ARB_NT/Tree/Dist Matrix V 1.0
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DESCRIPTION
This tool allows to calculate distance and similarity matrices
for the marked species. Conservation profiles can be established
and used as filters for column selection by other programs.
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Selection of columns:
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After selecting columns define how to treat ambiguities for
distance calculations:
Use the right mouse button to display the submenus
associated to the items below the 'distance matrix:'
prompt by pressing the respective buttons.
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don't count:
The particular position is not
included for binary distance
calculations if the symbol is
present in one or both sequences.
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use distance table:
the symbols are treated as unambiguous
residues
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Calculate profiles and matrices:
Use the right mouse button to display the 'CALCULATE'
menu and select 'markerline' (profile) or 'distance
matrix' by releasing the mouse button while the cursor
is positioned on the respective menu button.
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Display results:
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Use the right mouse button to display the 'VIEW'
menu and select 'species', 'markerline' or 'distance
matrix' by releasing the mouse button while the cursor
is positioned on the respective menu button. The names,
the aligment of the marked sequences and the
conservation profile, or the distance matrix are shown
within the display area, respectively.
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The profile:
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The fraction of sequences sharing most frequent residue
at a particular alignment position is shown as a number
to read bottom down. Alternatively, the profile can be
displayed as a curve by pressing the <toggle> button in
the left part of the window. It can be smoothed by
selecting a number from the 'smooth' menu (left part of
the window).
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Editing the aligned sequences and profiles, a name can
be selected by moving the cursor to it and pressing the
left mouse button. Pressing the <reference> button, the
respective sequence is used as a filter superimposed to
profile. This allows to exclude further positions from
subsequent calculations which are not occupied by bases
in the reference.
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Tha matrix:
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Editing the matrix, mean values can be calculated for
groups of organisms displayed as triangles (radial tree)
or rectangles (dendrogram) in a tree stored in the
database. The grouping currently or most recently
displayed is used for selecting sequences for the
calculation of mean values. Select a tree by pressing
the <grouping> button in the left area of the window.
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Save results:
To export distances and profiles (not graphs!!) to
ascii files, use the right mouse button to display the
'SAVE' menu and select the corresponding menu item by
releasing the mouse button while the cursor is
positioned on it.
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uncoded mline:
The positional conservation is encoded
by a sequence of letters: A = 1%,
B = 5%, ...., Z = 100%.
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bin mline:
Included and excluded columns are
indicated by 1 and 0, respectively.
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% dif. matrix:
Dissimilarity values.
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% sim. matrix:
Similarity values.
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phyl/prot distmat:
Corrected distances according Jukes and
Cantor (nucleic acid sequences only).
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pos. vari:
Number of different residues at the
particular alignment position.
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Reconstruct a tree:
Press the <NEIGHBOR> button. The tree is reconstructed
using the neighbour joining method and is stored in the
database as 'tree_neighbour'.
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Store profile in the database:
Press the <ARBSAVE> button to store any calculated
profile 0 / 1 encoded in the database (SAI). The profile
can be used as filter for other ARB tools.
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NOTES
A new version of the tool is under development.
It is recommended to calculate profiles here, to save them in
the database, and to reconstruct distance matrix trees using
'ARB_NT/Tree/Neighbour joining' in combination with the profile
as filter.
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EXAMPLESWARNINGS
Whenever text is typed to the window, press 'Return' on the
keyboard, to ensure that the information is recognized by the
program!!!
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BUGS |