IDV Typer

IDV lineage typing:

Infulenza D virus (IDV) is a novel member of Orthomyxoviridae family. The hemagglutinin-esterase fusion (HEF) gene is currently used to classify IDV into 5 lineages:
1) D/OK
2) D/660
3) D/Yama2016
4) D/Yama2019
5) D/CA2019
D/France2012 (tentative sixth lineage consisting of single isolate from France. D/bovine/France/2986/2012; GenBank ID: LN559126)


What is RTD? ?

Return Time Distribution (RTD) is an alignment-free approach for phylogeny. While most of the alignment-free methods use frequencies of k-mers in nucleotide sequences, RTD-based method utilises relative occurence of 'return times' or k-mers to summarise their compositions in the form of RTDs.


How RTD Works?
Pictorial view of the RTD based alignment-free method for phylogenetic tree reconstruction at k = 1:

Responsive image

Other RTD based typing servers:

1) RTD Phylogeny [PMID: 22820020]

2) DENGUE Subtyper [Nature Precedings]

3) WNV typer [PMID: 24388930]

4) RV-Typer [PMID: 26870949]

5) MuV Genotyping server [Immunome Research]