OCTOPAS

OCTOPAS is a fast and high-performance tool to reduce redundancy of large size phylogenetic datasets by referencing parent nodes.

The GUI version of OCTOPAS is now available here !

Description

• A Python tool which automatically prunes several leaves on phylogenetic trees to reduce their size and redanduncy by referencing parent nodes
• The input file format is Newick or NEXUS
• The output files are list of remaining leaves throughout the calculation and pruned phylogenetic tree
• Enjoy 🐙

Dependencies

• Python (v3.8 or more)
• phylotreelib (v1.18 or more)

Installation

This Python script requires phylotreelib package (https://pypi.org/project/phylotreelib/).

So, if necessary, implement this package by using pip command onto your environment:

[e.g.]

% pip install phylotreelib

Then, download the script octopas.py. Check if the tool works with -v or --version command:

[e.g.]

% python3 octopas.py -v

You can also download a small test phylogenetic tree data P69905_500_leaves.newick in demo direcotry, which is composed of 500 leaves of Human hemoglobin subunit alpha AA sequence and its highly redandunt homologous sequences.

Input file format

The input tree data must be in Newick or NEXUS format. Visit below for more information about these formats:

• Newick (https://evolution.genetics.washington.edu/phylip/newicktree.html)
• NEXUS (http://wiki.christophchamp.com/index.php?title=NEXUS_file_format)

Usage

Basically, this tool requires input tree data with -i or --input command-line argument and output files prefix with -o or --output. A minimal example of usage is below:

[e.g.]

% python3 octopas.py -i P69905_500_leaves.newick -o output

Type -h or --help to see all the options supported:

Option	Option type	Description
-i or --input	String	Input file name, REQUIRED
-o or --output	String	Output file name prefix, REQUIRED
-O or --outdir	String	Output directory name, if it is empty, all output files are saved in current directory
-f or --format	String	Format of input file, newick or nexus
-n or --NL	Integer	Number of leaves remain, 3 or more, default 3
-r or --RTL	Real	Threshold of relative tree length, at range of [0, 1], default 0.95
-F or --outfmt	String	Format of output file, newick or nexus
-R or --resolution	Integer	Resolution of leaf pruning, 1 or more, default 1
-s or --silent	Flag	If true, program does not show any logs on terminal during calculation
-v or --version	Flag	Print current version, ignore all other arguments
-h or --help	Flag	Print this help, ignore all other arguments

Output

This tool generates 5 types of output file:

File name	Description
<output prefix>.log	Execution log of the program
<output prefix>.tsv	TSV file recods remaining Leaves number, relative tree length and pruned leaf in each iteration
<output prefix>_pruned_leaves.txt	List of pruned leaves
<output prefix>_remaining_leaves.txt	List of remaining leaves
<output prefix>_tree.<tree format>	Output pruned tree in Newick or NEXUS format

Tutorial

Pruning leaves based on Relative Tree Length (RTL)

In this demo, the test data P69905_500_leaves.newick in demo directory is used. The program was executed to this test data with options -n = 3 and -R = 1, which number of the leaves remain is set at 3 with resolution in each iteration at 1:

% python3 octopas.py -i P69905_500_leaves.newick -o output -n 3 -R 1

The X axis represents number of the remaining leaves and the Y axis is RTL in each iteration. The dot plot shows that number of leaves remain is 248, while the RTL (total branch length of pruned tree / total branch length of original tree) is 0.95, implying that OCTOPAS pruned 252 leaves and retained the rest 248, while the 95% of divergence of the tree was preserved.

Improvement of Relative Closest Branch Length (RCBL)

RCBL (average distance of leaves to their closest leaves in trimmed tree / average distance of leaves to their closest leaves in original tree) is also calculated as another performance evaluation. In this demo, to what extent the RCBL in the pruned tree can improve compared to the original tree's throughout the execution of the tool, while the stop option is set at 0.95 of RTL:

% python3 octopas.py -i P69905_500_leaves.newick -o output -r 0.95

The horizontal violin plot shows that the Average Closest Branch Length (ACBL) of the original tree (n=500) is 0.092 and ACBL of the pruned tree (n=248) is 0.221. Hence, the RCBL is about 2.412 (the exact number might be different as both of ACBLs are rounded at digit 3), implying that the average of branch lengths between the leaves and their closest leaves improves more than twice throught the execution of OCTOPAS, while 95% of divergence of the phylogenetic tree is preserved.

Queries, issues and reports

If you have any inquiries, requests for new functionalities, reports on errors, or concerns related to the most recent release of OCTOPAS, kindly utilise the issues section positioned at the upper-left corner of the GitHub repository.