Main topics:

Neighbour joining

OCCURRENCE
DESCRIPTION
Calculate compressed matrix
Automatic calculation
NOTES
WARNINGS
BUGS

OCCURRENCE

ARB_NT/Tree/Build tree from sequence data/Distance matrix methods/Distance matrix + ARB NJ

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.

Mark all interesting species.
Select all or marked species from the 'Select Species' menu of the 'NEIGHBOUR JOINING' window.
Select Alignment from the 'Select Alignment' subwindow of the 'NEIGHBOUR JOINING' window.
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.
Define Weights: @@@ not implemented
Select rate matrix (only implemented for some corrections; see ´User Defined Distance Matrix´)
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.
Possible settings are "" (empty), "." and ".-".
- "" treats dots as separate gap-type (i.e. '.' vs. '-' counted as mutation)
- "." does not count dots (over-rates gaps running over multiple columns)
- ".-" does not count gaps (ignores insertions and deletions)
```
Note: This setting is ignored when using a ´User Defined Distance Matrix´ or
      if Kimura correction is selected.
          
```
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.

from selected tree:
This is NOT a distance correction! By selecting 'from selected tree' distances are not calculated using sequence data. Instead they are extracted from the tree currently selected in the 'Trees in Database' selection list.

The distance between two species is defined as the sum of the lengths of all branches that connect these two species.

Please note that this is an experimental feature. The distances between two species are not directly based on the sequence differences between these two species. Instead they reflect the evolutionary distance assumed by the tree reconstruction algorithm used to build the tree.

The distances extracted from a tree are expected to be (slightly) bigger than the distances directly calculated from the sequences. This seems reasonable, because it is very unlikely, that evolution always took the shortest possible way (which is represented by the direct sequence distance). This effect increases for more distant (unrelated) species, reflecting the indirections evolution most likely made.

Please note:
the other correcting functions are in an experimental state. Wait for new release.!!!
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.
Press the 'CALCULATE TREE' button
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

You may select a tree to calculate a compressed matrix. A compressed matrix contains columns for all folded groups visible in the displayed tree (i.e. not for unfolded groups and not for folded groups inside other folded groups).

Species inside such groups are NOT listed as single entries.

The distance shown for each group is the arithmetic average of of the distances of all contained species.

Automatic calculation

There are two toggles in the ARB_DIST main window allowing to trigger instant recalculation:

'Auto recalculate' will force recalculation of the matrix
'Auto calculate tree' will force calculation of the tree
If 'Auto calculate tree' is checked, the tree will be calculated whenever the matrix has been updated.

If 'Auto recalculate' is checked, the matrix will be recalculated whenever any input changes, e.g. if
the filter is changed (or its underlaying SAI changes),
the excluded columns change,
the user defined matrix changes,
the correction is changed,
the sequence data changes or species marks change or
the tree selected for compression or sorting changes or a different tree is selected.

As you might have guessed, this is only useful for smaller sets of sequences.

Some suggestions:

You might for example display the resulting NJ tree in one window and play with distance parameter to instantly see their effect on the tree.

Or you may unmark unwanted species/subtrees in the tree display.

Or you might align sequences to see the effect on the resulting topology.

NOTES

Computing time can be estimated using the following formula:

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

Example: Sparc 10, 74 Sequences, length 8000 characters
         -> 10 Seconds

WARNINGS

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

Distance values calculated without distance correction are strictly inside range [0.0 .. 1.0]. Same is true for 'similarity' distance "correction". With distance corrections, the range does vary depending on the correction method.