Metadata-Version: 2.1
Name: rtd_phylogeny
Version: 0.0.32
Summary: Molecular phylogeny analysis using Return time distribution (RTD) based alignment-free sequence analysis method
Home-page: https://github.com/pandurang-kolekar/rtd-phylogeny
Author: Pandurang Kolekar
Author-email: pandurang.kolekar@gmail.com
License: UNKNOWN
Description: ![alt text](https://github.com/pandurang-kolekar/rtd-phylogeny/raw/master/data/RTD_Phylogeny.jpeg "RTD logo (c) Pandurang Kolekar 2017")
        
        # RTD Phylogeny
        Molecular phylogeny analysis using Return time distribution (RTD) based alignment-free sequence analysis method
        
        ### Author
        Pandurang Kolekar, PhD Bioinformatics
        
        ![alt text](https://orcid.org/sites/default/files/images/orcid_16x16(1).gif "Logo ORCID") http://orcid.org/0000-0003-0044-0076
        
        E-mail: pandurang.kolekar@gmail.com
        
        Website: [http://biosakshat.wixsite.com/pandurang-kolekar](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<sup>k</sup>_. 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](https://www.ncbi.nlm.nih.gov/pubmed/22820020)
        
        ## Requirements
        
        Tested on Python 3.7
        Please refer to requirements.txt file
        
        ## Quick Start
        ```shell
        python src/rtd_phylogeny.py --help
        python src/rtd_phylogeny.py --version
        python src/rtd_phylogeny.py --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/](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](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](https://www.ncbi.nlm.nih.gov/pubmed/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](https://github.com/pandurang-kolekar/rtd-phylogeny/issues)
        
        * E-mail us at rtd.phylogeny@gmail.com
        
        * Fill the feedback form for the RTD Phylogeny server: Available [here](https://docs.google.com/forms/d/e/1FAIpQLSel8RYKGQ3IIUxwjo0HgrDUyNv0ClNNwQETvguLUA2VYt0Odw/viewform)
        
        Your feedback is highly valuable! 
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
