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 (only implemented for some corrections; see ´User Defined Distance Matrix´)
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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.
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 tw
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