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Last update on 04. Dec 2013 .
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Neighbour joining

OCCURRENCE

ARB_NT/Tree/Neighbour joining

 

DESCRIPTION

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.

  1. Mark all interesting species.
  2. Select all or marked species from the 'Select Species' menu of the 'NEIGHBOUR JOINING' window.
  3. Select Alignment from the 'Select Alignment' subwindow of the 'NEIGHBOUR JOINING' window.
  4. 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.
  5. Define Weights: !!! not implemented !!!
  6. Select rate matrix: !!! not implemented !!!
  7. 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.
  8. 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.
    • none:
              Differences/Sequence length. May be a good
              choice for short sequences (length < 300 )
    • similarity:
              1.0 - Differences/Sequence_Length
    • jukes-cantor:
              Accounts for multiple base changes, assumes
              equal base frequencies.
              Good choice for medium sized sequences
              ( 300 - 1000/2000 sequence length )
    • felsenstein:
              Similar to jukes-cantor transformation. Allows
              unequal base frequencies.
              ( length > 1000/2000 )
    • olsen:
              As Felsenstein, except the base frequencies are
              calculated for each pair of sequences.
    • !!! The other correcting functions are in an experimental state.
                      Wait for new release.!!!

  9. 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.
  10. Press the 'CALCULATE TREE' button
  11. 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

 

NOTES

Read the NDS help text

 

NOTES

Computing time can be estimated using the following formula:

time = (Sequence_Length * Nr.of.Spec * Nr.of.Spec)/ Computer Power

Examples:       Sparc 10,
                74 Sequences, length 8000 characters

> 10 Seconds

 

WARNINGS

Don't try to build a tree with the 'similarity' distance correction selected.

 

BUGS

None