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Last update on 25. Nov 2018 .
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Partial sequences

OCCURRENCE

General

 

DESCRIPTION

Species should contain an entry 'ARB_partial' specifying whether the associated sequence is a "full sequence" or a "partial sequence".

If 'ARB_partial' is 1 then the sequence is considered partial.

There's a special function to add partial sequences (see ´Add marked partial species´).

 

NOTES

There are several function to find and mark species with partial or full sequence in the Species menu.

 

EXAMPLES

Attraction of partial sequences (when added as full sequence):

Species1       .....NNNNNNNNNNN.............................
Species2       .......................NNNNNNNNNNNNNN........

The calculated distance between 'Species1' and 'Species2' will be ZERO when they are added as full sequences and as a result they will group together.

Adding them as partial sequences will avoid that problem.

 

WARNINGS

Partial sequences cannot be used to calculate trees. Currently this isn't forbidden, but it's highly recommended not to do that.

Instead remove all species with partial sequences from the tree, then optimize the tree and afterwards add the removed species again using ´Add marked partial species´.

 

BUGS

No bugs known