Molecular phylogeny analysis using Return time distribution (RTD) based alignment-free sequence analysis method
Pandurang Kolekar, PhD Bioinformatics
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E-mail: [email protected]
Website: http://biosakshat.wixsite.com/pandurang-kolekar
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*4k. 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
Tested on Python 3.7 Please refer to requirements.txt file
pip install rtd-phylogenypython -m rtd_phylogeny --help
python -m rtd_phylogeny --version
python -m rtd_phylogeny --fastaFile <input_file> --seqType N --kmerSize 3The web server for RTD-based phylogeny is available from http://bioinfo.unipune.ac.in/RTD/.
The standalone Perl executables for RTD Phylogeny program are available from http://bioinfo.unipune.ac.in/RTD/download.html.
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
Please do feel free to give your comments / suggestions about this package by any of the following mode.
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Report an issue on this GitHub repository here
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