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Last update on 25. Nov 2018 .
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Select Filter

OCCURRENCE

ARB_NT/Tree/Neighbour joining/Select Filter

 

DESCRIPTION

Any sequence of symbols stored as 'sequence associated information' ('SAI') can be selected from the 'Select a Filter' subwindow and used as a filter for the in or exclusion of alignment columns for treeing. If any species is selected, you may use it's sequence for filter. It's name will be displayed just before the SAI names.

The characters of the filter which define columns to exclude have to be defined in the respective input field.

Additionally or alternatively you may define the absolute column range to be used (a range from 0 to 0 means 'use whole sequence').

The selected filter is displayed in the subwindow on the bottom.

All bases may be simplified, leaving only transversions and simplified amino-acid-groups, allowing transversion parsimony/fdnaml/distmethods

 

NOTES

Any nucleotide sequence can be copied to SAI (sequence associated information) (ARB_NT/Species/Info/SPECIES/Convert to SAI) and then used as a filter.

Multiple filters may be combined. In this case only those columns are used that are selected by ALL filters.

 

EXAMPLES

Include only positions which are occupied by a residue within the E. coli sequence:

  1. Select 'ECOLI' from the 'Select a Filter' subwindow.
  2. Type non-nucleotide symbols to the 'Exclude Column' subwindow (.-).

Include only non-base paired positions:

  1. Select 'HELIX' from the 'Select a Filter' subwindow.
  2. Type base pair symbols to the 'Exclude Column' subwindow ([<>]).

Include only positions which have been unambiguously determined within a particular sequence:

  1. Select the species and convert it to 'SAI' using ´Convert Species to SAI´.
  2. Select the new 'SAI' from the 'Select a Filter' subwindow.
  3. Type non-nucleotide and ambiguity symbols to the 'Exclude Column' subwindow (.-acguRYS ....).

 

WARNINGS

None

 

BUGS

No bugs known