PB Distance

--distance, -dis

Description

When presented with different trees containing the same (or a similar) set of taxa, it is sometimes useful to describe their relative difference. The three metrics available in PhyloBuddy are:

• Unweighted Robinson-Foulds
  • Distance is based on the minimum number of operations required to convert one tree into the other
• Weighted Robinson-Foulds
  • Takes edge length into account
• Euclidean distance
  • The square root of weighted edges

If more than two trees are included, then an all-by-all comparison will be carried out to generate values for every possible pairing.

Arguments

Calculation method ( {wrf | uwrf | ed} )

Optional. Choose an algorithm to generate your distance metrics.

• 'wrf' = weighted_robinson_foulds (default)
• 'uwrf' = unweighted_robinson_foulds
• 'ed' = euclidean_distance

Examples

input file: fir.nex

#NEXUS

BEGIN TAXA;
    DIMENSIONS NTAX=8;
    TAXLABELS
        firSA26b
        firSA24a
        firSA24b
        firSA25a
        firSA26a
        firSA25b
        firSA23a
        firSA23b
  ;
END;

BEGIN TREES;
    TREE 1 = [&U] (firSA26b:3.0,firSA24a:1.0,firSA24b:1.0,firSA25a:1.0,firSA26a:1.0,firSA25b:2.0):2.0;
    TREE 2 = [&U] (((firSA24b:3.0,firSA25b:2.0):2.0,firSA24a:2.0):1.0,((firSA25a:1.0,firSA23a:1.0):2.0,firSA23b:3.0):1.0):3.0;
    TREE 3 = [&U] ((firSA26a:1.0,firSA25a:1.0,firSA26b:1.0):1.0,firSA25b:1.0,firSA24a:1.0,firSA24b:1.0):1.0;
    TREE 4 = [&U] (((((firSA24a:1.0,firSA24b:1.0):4.0,firSA26b:1.0):1.0,firSA26a:2.0):1.0,firSA25a:1.0):4.0,firSA25b:3.0):1.0;
END;

usage example 1

$: pb fir.nex -dis

output

Tree 1	Tree 2	Value
tree_1	tree_2	20.0
tree_1	tree_3	5.0
tree_1	tree_4	15.0
tree_2	tree_3	21.0
tree_2	tree_4	31.0
tree_3	tree_4	14.0

usage example 2

$: pb fir.nex -dis 'uwrf'

output

Tree 1	Tree 2	Value
tree_1	tree_2	9
tree_1	tree_3	1
tree_1	tree_4	3
tree_2	tree_3	10
tree_2	tree_4	12
tree_3	tree_4	4

usage example 3

$: pb fir.nex -dis 'ed'

output

Tree 1	Tree 2	Value
tree_1	tree_2	6.48074069840786
tree_1	tree_3	2.6457513110645907
tree_1	tree_4	7.0
tree_2	tree_3	6.244997998398398
tree_2	tree_4	9.1104335791443
tree_3	tree_4	7.483314773547883