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Last update on 25. Nov 2018 .
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Add species without optimizing topology

OCCURRENCE

ARB_NT/Tree/Add Species to Existing Tree/ARB Parsimony (Quick add marked)

ARB_PARSIMONY/Tree/Add Species to Tree/Add Marked Species

ARB_PARSIMONY/Tree/Add Species to Tree/Add Selected Species

ARB_PARSIMONY/Tree/Add Species to Tree/Remove & Add Marked Species

 

DESCRIPTION

All affected 'species' are positioned according to maximum parsimony criteria. The current tree topology will not be optimized after insertion.

In case of 'Add Selected Species' the currently ´Selected species´ gets inserted. The other functions always work on all 'marked species'.

In case of 'Remove & Add Marked Species' any marked species are first removed from the tree and then inserted again. The other functions only add those marked species which are not already present in the tree.

 

Full length vs partial sequence data

This function only works correct when adding full-length sequences (FLS), where full-length here applies to the resulting positions after applying the selected alignment filter(s).

Any partially missing sequence data will be considered an deletion and adds extra distance between full- and partial sequences.

One common effect of doing so, is that partial sequences often group together although they obviously are not (parts of) near relatives, just because they do not share (enough) alignment regions.

To avoid that problem

  • do not use partial sequence data (recommended) or
  • (if you really have to) declare and handle partial sequence data as such, by using ´Add marked partial species´.

 

Tree degeneration

As no topology optimization takes place here, the tree will tend to degenerate while you add more and more species, i.e. the tree will continuously diverge from an optimized topology build upon the same set of species.

Nevertheless this function has proven useful to determine the phylogenetic position of new/custom sequences in an optimized tree. But you should always be aware that, the more often you add sequences this way, the worser your topology will get.

Probably you may want to optimize your tree from time to time. See ´Tree optimization´ for howto.

 

Insertion order

Until arb-6.0.x species with more base positions were added before such with less bp.

Starting with arb-6.1 all species are added independently, i.e. there is no explicit insertion order (see exception below). The performance has been improved dramatically, especially when adding many species and/or when adding into big trees.

If multiple species are added to the same position in the tree, they form a subtree which will be optimized afterwards.

Exception:

If the number of added species exceeds 50% of the size of the tree (e.g. if adding more than 1000 species to a tree containing 2000 sp.), the species will be devided into multiple sets and then these sets will be inserted one after each other. Longer sequences will be added earlier in this case.
 

NOTES

The current parsimony value (see ´Parsimony value´) is displayed after the 'Current Par' prompt in the upper part of the 'ARB_PARSIMONY' window and the 'Message' window (pops up while calculating).

 

EXAMPLES

None

 

WARNINGS

The phylogenetic information conferred by the new sequence(s) is not used for global tree optimization.

 

BUGS

No bugs known