Reconstructs a tree for all or marked species by first
calculating binary distances and subsequently applying the
neighbour joining method.
The tree topology is stored in the database and can be displayed
within the tree display area of the 'ARB_NT' window.
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Mark all interesting species.
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Select all or marked species from the 'Select Species' menu
of the 'NEIGHBOUR JOINING' window.
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Select Alignment from the 'Select Alignment' subwindow of
the 'NEIGHBOUR JOINING' window.
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Display the 'Select Filter' window by pressing the button
after the 'Filter' prompt and define an alignment-
associated mask which defines alignment positions to
include for treeing.
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Define Weights: !!! not implemented !!!
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Select rate matrix: !!! not implemented !!!
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Type characters for the exclusion of alignment postions to
the 'Exclude Column' subwindow. The positions are
excluded from the calculation of binary distance values
if one of the specified characters is present in one or
both sequences. The described function acts as a second
filter and affects only the particular sequence
pairs, not the whole alignment.
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Select the type of distance correction from the 'Distance
Correction' submenu. You can use the program to detect
the best correction for you by pressing the AUTODETECT
button.
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none:
Differences/Sequence length. May be a good
choice for short sequences (length < 300 )
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similarity:
1.0 - Differences/Sequence_Length
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jukes-cantor:
Accounts for multiple base changes, assumes
equal base frequencies.
Good choice for medium sized sequences
( 300 - 1000/2000 sequence length )
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felsenstein:
Similar to jukes-cantor transformation. Allows
unequal base frequencies.
( length > 1000/2000 )
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olsen:
As Felsenstein, except the base frequencies are
calculated for each pair of sequences.
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!!! The other correcting functions are in an experimental state.
Wait for new release.!!!
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Select a name for the tree from the 'Trees in Database'
subwindow or type a new tree name.
The tree name has to be 'tree_*'.
An existing tree with that name will be deleted.
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Press the 'CALCULATE TREE' button
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Now you may display the new tree in the ARB_NT main window
by selecting its name from the <Tree/Select> subwindow.
If its name is already selected, you will not need to
reselect it.
The distance matrix can be written to an ascii file:
Press the <SAVE MATRIX> button to display the 'SAVE
MATRIX' window. Select a file from the 'Directories
and Files' subwindow or type a file name to the 'FILE
NAME' subwindow. Press the <SAVE> button.
The suffix displayed in the 'SUFFIX' subwindow is added
to the typed file name and defines the selection of
files listed in the 'Directories and Files' subwindow.
@@@ Calculate Compressed Matrix
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