You may use DNAsp for haplotype identification

Dear Ghosh,

I really appreciate your suggestion.

Thank you.

A little more context would be helpful. Do you have high-throughput sequencing data, or Sanger sequencing? For high-throughput data, GATK (https://gatk.broadinstitute.org/hc/en-us) is a standard pipeline for calling SNPs and haplotypes. I also like ANGSD as well. FreeBayes is another commonly used genotyper.

Dear Justin,

I have high throughput sequencing data.

Thanks for the follow-up Nisha. The options I suggested would probably be your best bet.

For ddRADseq, dDocent works well followed by radhaplotyper