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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.

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