treedist

Rapid calculation of pathlength distances between taxa on phlyogenetic trees

If you use this tool, please reference this DOI:

This comprises two tools that are used to calculate pathlength distance on phylogenetic trees.

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treedist_pair:

This software returns the distance between two branches of a tree (including internal branches).

This softtware is called with the name of the file containing the tree, and the names of the two branches

Usage: treedist <Tree file name> <Branch name> <Branch name>

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treedist_all:

This software returns the pathlength distances between all terminal branches of a tree.

This softtware is called with the name of the file containing the tree

Usage: treedist_all <Tree file name> <matrix|vector|text>

Optional output format specification: matrix (default) or vector.

If a text string is specified instead of "matrix" or "vector" it should be a whole or part of a taxon name.

In this case treedist_all will only print distances to or from taxa that match the text string (in vector format).

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To Compile

cc -o treedist_pair.c -o treedist_pair
cc -o treedist_all.c -o treedist_all

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Example usage:

With the provided example tree file 'testtree.ph'

((A:0.01,B:0.02)I5:0.1,(((C:0.02,D:0.01)I2:0.1,E:0.001)I3:0.1,F:0.003)I4:0.05);

which looks like this:

To calculate the pathlength distances between:

A and B

treedist_pair testtree.ph A B

which returns '0.030000'

A and Internal branch I2

treedist_pair testtree.ph A I2

which returns '0.360000'

All distances between all terminal taxa

treedist_all testtree.ph matrix

Which returns a file called 'testtree.ph.dist' containing:

  	A	B	C	D	E	F
A	0.000000	0.030000	0.380000	0.370000	0.261000	0.163000
B	0.030000	0.000000	0.390000	0.380000	0.271000	0.173000
C	0.380000	0.390000	0.000000	0.030000	0.121000	0.223000
D	0.370000	0.380000	0.030000	0.000000	0.111000	0.213000
E	0.261000	0.271000	0.121000	0.111000	0.000000	0.104000
F	0.163000	0.173000	0.223000	0.213000	0.104000	0.000000

To return the same information but in vector (pairwise) format:

treedist_all testtree.ph vector

which will return:

A	B	0.030000
A	C	0.380000
A	D	0.370000
A	E	0.261000
A	F	0.163000
B	C	0.390000
B	D	0.380000
B	E	0.271000
B	F	0.173000
C	D	0.030000
C	E	0.121000
C	F	0.223000
D	E	0.111000
D	F	0.213000
E	F	0.104000

NOTE that each pair-wise distance is only reported once in vector format.

All distances from taxa matching the text string "A" to everything else

treedist_all testtree.ph A

Which returns in vector format:

A       B       0.030000
A       C       0.380000
A       D       0.370000
A       E       0.261000
A       F       0.163000

This option allows the full name or partial names to be used, so if you have the taxa "Pan paniscus" and "Pan troglodytes" in your tree and you can specify

treedist_all TREE Pan

To only output (in vector format) the distances between all species matching the text string "Pan" to all other species.