Description of the server:
RTD Phylogeny is a Return Time Distribution (RTD) based alignment-free approach for phylogeny of genomic sequences. While most of the alignment-free methods use frequencies of k-mers in genomic sequences, RTD-based method utilises relative occurence or 'return times' of k-mers to summarise their compositions in the form of RTDs. The statistical parameters of these RTDs are then used to transform sequences into respective numeric vectors. The Euclidean type distance function is then used to derive pairwise distance matrix, which is subsequently given as an input to Neighbor-joining method to infer phylogenetic tree.
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Applications of RTD-based method: Visit other servers.
The applications of RTD-based method have been extended for large-scale subtyping of viruses such as Mumps virus, Dengue virus, West Nile virus etc.
Citation information:
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. [PMID: 22820020]RTD Phylogeny server has been developed at Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), funded by Department of Biotechnology (DBT), Government of India under the Centre of Excellence grant. Pandurang Kolekar acknowledges the DBT- Bioinformatics National Certification (BINC) fellowship.