RTD Phylogeny

Molecular phylogeny analysis using Return time distribution (RTD) based alignment-free sequence analysis method

Author

Pandurang Kolekar, PhD Bioinformatics

http://orcid.org/0000-0003-0044-0076

E-mail: pandurang.kolekar@gmail.com

Website: http://biosakshat.wixsite.com/pandurang-kolekar

Introduction

Return time distribution (RTD) is a method for alignment-free phylogenetic analysis using nucleotide / protein sequences. The method first computes the RTDs of k-mers and summarize them using the parameters of RTDs viz. mean and standard deviation for each of the sequences. Thus, each sequence is converted into a numeric vector of the size 2*4^k. The pair wise distance between numeric vectors of sequences is calculated using Euclidean distance function. The pairwise distance matrix, thus obtained is given as an input to Neighbor-joining clustering algorithm to reconstruct phyogenetic tree.

The statistical details of the method are described in Kolekar et al. 2012

Requirements

Tested on Python 3.7 Please refer to requirements.txt file

Installation

pip install rtd-phylogeny

Quick Start

python -m rtd_phylogeny --help
python -m rtd_phylogeny --version
python -m rtd_phylogeny --fastaFile <input_file> --seqType N --kmerSize 3

Web Server

The web server for RTD-based phylogeny is available from http://bioinfo.unipune.ac.in/RTD/.

Perl Executables

The standalone Perl executables for RTD Phylogeny program are available from http://bioinfo.unipune.ac.in/RTD/download.html.

Citation Information

If you find this program useful please cite it as following,

Kolekar P., Kale M., Kulkarni-Kale U., Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping, Molecular Phylogenetics and Evolution, (2012) 65(2): 510-522

PubMed ID: 22820020

Feedback

Please do feel free to give your comments / suggestions about this package by any of the following mode.

• Report an issue on this GitHub repository here

• E-mail us at rtd.phylogeny@gmail.com

• Fill the feedback form for the RTD Phylogeny server: Available here

Your feedback is highly valuable!