About DefIn

DefIn is a python based program for computing the Deformity Index of a phylogenetic tree based on either partial or complete knowledge of the relationships among the species.

Required packages

The DefIn is developed on python 2.7 and Linux based system. So this program is only compatible for python 2.7. The other prerequisite is,

• Dendropy v4.4.0

Create the environment

For executing the DefIn we recommend to create a separate environment in anaconda. The image of the required environment (.yml) is given in this package. First create the environment and activate it by executing the following commands,

conda env create -f dienv.yml

conda activate diEnv

We recommend to verify the installed package list in the diEnv by executing conda env list.

The DefIn options

DefIn can only be executed through the command prompt. It is necessary to make all the python file executable before running the program (use chmod +x *.py). The command to execute the DefIn from the command prompt is as ./DefIn.py with the command line arguments. The options are as follows,

• -i Mention the file that contains the target tree (in NEWICK format). Please refer to the Sample_Input/TargetTree.nwk for the detail format of the file.

• -t This is a boolean option. If this option is provided then the program will consider the reference tree mentioned by the option -r, else the program will consider the list of clades mentioned by the option -c. For further detail please refer to option -c and -r.

• -c Mention the file that contains the list of clades. The clade is represented as the list of species separated by a comma. Each line contains a single clade. Please refer to the Sample_Input/Clades.txt for the detail format of the file.

• -r Mention the file that contains the reference tree (in NEWICK format). The reference tree can be both resolved (binary) or unresolved. Please refer to the Sample_Input/RefTree.nwk for the detail format of the file.

Execution of DefIn

./DefIn.py -i [target tree] [ -c | [ -r [reference tree] -t ] ]

• Minimal command:

./DefIn.py -i [target_tree]

In the minimal command, the script considers Species_Class.py placed in the same directory. Please refer to the Species_Class.py for the detail format of the file.

The DefIn can execute in two different modes:

• Using list of clades: In this command, the script considers the file contains a list of clades. The list of clades can be provided in two ways,

  (a) (Default) providing the list of clades in Species_Class.py placed in the same directory.

  (b) providing the list of clades as a text file. For this use the option -c to mention the text file.

• Using reference tree: In this command, the script considers the file contains a reference tree to compute the Deformity Index. For this the option -t need to put and the reference tree file should be mentioned using -r option.

** A sample command file is provided with this package. The shell script file name Sample_Script.sh, contains the sample code and can be executed by changing the variables accordingly.