Indel-K2P: a modified Kimura 2 Parameters (K2P) model to incorporate insertion and deletion (Indel) information in phylogenetic analysis

Asim Kumar Mahadani, Shashank Awasthi, Goutam Sanyal, Partha Bhattacharjee and Sanjeev Pippal

Cyber-Physical Systems, 2022, vol. 8, issue 1, 32-44

Abstract: Evolutionary models are widely used to estimate the evolutionary relationship between the various biological taxa . Majority of the existing evolutionary models ignore insertion and deletion (indel) event, which reduces the computational difficulties, but at the same time, it causes loss of valuable phylogenetic information. In this study, we have developed a modified Kimura 2 parameters (K2P) model to utilise the indel information in phylogenetic tree construction especially in case of low substitution rate sequences Indel rich highly similar DNA sequences (trnL-trnF intergenic spacer region) of Phalaenopsis were collected from Genbank and to test the efficiency of the model in phylogenetic. Our developed Indel-K2P model and K2P model were implemented in MATLAB and calculated the bootstrap value and Robinson-Foulds (RF) distance to test the confidence and accuracy of phylogenetic tree topology. The phylogenetic trees constructed within the framework of Indel-K2P model, exhibited 92.66% accuracy and 40.9% root node confidence while the K2P model without indel shows less accuracy and less root node confidence. Our results indicate that modified Kimura 2 parameters with indel (Indel-K2P) model performed better than Kimura 2 Parameters (K2P) in phylogenetic tree construction for indel rich DNA sequences.

Date: 2022
References: Add references at CitEc
Citations:

Downloads: (external link)
http://hdl.handle.net/10.1080/23335777.2021.1879274 (text/html)
Access to full text is restricted to subscribers.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:taf:tcybxx:v:8:y:2022:i:1:p:32-44

Ordering information: This journal article can be ordered from
http://www.tandfonline.com/pricing/journal/tcyb20

DOI: 10.1080/23335777.2021.1879274

Access Statistics for this article

Cyber-Physical Systems is currently edited by Yang Xiao

More articles in Cyber-Physical Systems from Taylor & Francis Journals
Bibliographic data for series maintained by Chris Longhurst ().