Finding SNP between two genes sequenced by sanger sequencing

Question

[Shanika]

I have DNA sequences of a gene from two closely related Swallow species. I need to find the SNP between the two species. How can I do this without using a reference? The sequencing was done using Sanger sequencing Thank you in advance

Answer 1

[Asaf]

I would use good old global alignment. needle from EMBOSS