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

3. 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