How to use the phylogenetic_diversity.py

[LuckyFeiX]

I was confused that one of the scripts had no instructions, and actually found it so useful. So I hope to get the answer from the author of this software.

[donovan-h-parks]

GenomeTreeTk and associated scripts are not recommended for public use. The code is provided for those wishing to investigate it, but we do not currently have the resources to document and maintain this software package. Sorry I can't be of direct help.

[donovan-h-parks]

Hi. Have you tried to run this script via the GenomeTreeTk command line interface:

genometreetk pd -h

For most uses, it simply requires an input tree in Newick format and a plain text file listing the genomes you wish to calculate PD for.

[LuckyFeiX]

yeah，but i don't know the input data and parameters

	Fei Xie Nanjing Agricultural University

College of Animal Science and Technology xiefei_njau@163.com |

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On 10/25/2019 22:32, Donovan Parks wrote:

Hi. Have you tried to run this script via the GenomeTreeTk command line interface:

genometreetk pd -h

For most uses, it simply requires an input tree in Newick format and a plain text file listing the genomes you wish to calculate PD for.

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[donovan-h-parks]

Addressed via personal communication with toy example:

genometreetk pd my_tree.tre my_taxa.lst

my_tree.tree: is a phylogenetic tree in Newick format my_taxa.lst: is a plain text file with one taxa per line

Example tree: ((a:1,b:1):2,c:2); Example taxa file: a c

This calculates the phylogenetic diversity spanned by taxa a and c. The output is:

No. Taxa PD Percent PD Full tree 3 6.00 100.00% Outgroup taxa (PD) 1 3.00 50.000% Ingroup taxa (PD) 2 5.00 83.333% Ingroup taxa (PG) 2 3.00 50.000%

This indicates the full tree has a branch length of 6 and that the two taxa a and c have a branch length of 5 which is 83.3% of the total. These two taxa add a total branch length (i.e. phylgenetic gain) of 3 which is 50%.