**2.4. Sequence analysis and multiple sequence alignment**

Pairwise sequence alignments were carried out using NCBI-BLASTN 2.2.5 version & PSI BLAST. Multiple sequence alignments were done using the MUSCLE 3.6 software and CLUSTALW (1.82). Analysis, manipulation, conservation plots, positional entropy plot and conserved region analysis was done using the BIOEDIT package. Variable sites were extracted from the multiple sequence alignment using the MEGA 3.1 package **[12]**.

## **2.5. Phylogenetic analysis**

Phylogenetic model selection was done using the FINDMODEL server available from the HCV LANL database at (http://hcv.lanl.gov/ /content/hcv-db/findmodel/). A Bayesian phylogenetic tree was constructed by Markov chain Monte Carlo (MCMC) method as implemented in the MR BAYES 3.1 package using the Hasegawa-Kishino-Yano plus Gamma model HKY+G substitution model with an invariant four category gamma distribution among sites. A 50% consensus tree was generated and the analysis was repeated two times. Maximum parsimony tree was conducted using MEGA version 4, with 1000 bootstraps for reliability.

The mean overall, within group and between groups genetic distances were done using the MEGA 4.0 software **[12]**.
