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PD_stats

A project designed with algorithms to compute PD Statisttics- Minimum, Maximum, Average, Variance on a binary nexus phylogenetic tree

Requirements

  • Python 3.7

Packages Used

  • dendropy
  • Bio
  • decimal
  • scipy
  • numpy
  • argparse

the statistic arguements are as follows -fmin:- min -fmax:- max -favg:- avg -fvar:- var -fhot:- hotspot measure -fall:- computes all the statistics above

To run this tool on a nexus tree please follow the steps below

  1. place nexus binary treefile in the same directory as the project
  2. run pdstat.py with the following arguemenets:- treename, (int)k, min/max/avg/var
  • example : pdstat.py treename.tre 10 -fmax The example above runs pdstat.py on the tree treefile where 10 is the user input and wants to finds the minPD

    Note:- the User can run multiple functions on the the treefile, ex. pdstat.py treename.tre 10 -fmax -fmin

  1. There will be a file named "annotated_tree_nex" with the clades annotated with the minPD at clade

Test files t50.tre,t100.tre,t200.tre,tt300.tre,t400.tre are also present in the directory for tests.

Scalability of Algorithms:- The above algorithms were run on different trees with the number of leaves ranging from 1000 to 10000 taxa with k = n image