Which Sequence aligners to use?

[NGS_New_User]

Hello wise people,

I'm trying to align a sequence of a gene that is present in two related species. Each of the genes in either species has SNPs in various positions. My goal is to find if the SNPs are in similar positions, or better yet align with each other.

In one species the length is ~700 bases and the other ~1200bases.
I didn't know how to go about with it, so with trial and error, I tried using different aligners [clc, bioedit (pairwise alignment, global and clustalw), muscle]...and they are all giving me different results.

I was just wondering what might be causing the differences because I am presuming I am doing something wrong.

Which other aligners would you suggest I use for this. Should I do global alignment or local alignment?

[swbarnes2]

If they differ in length that much, there probably isn't one easy way to align them, and that's why you are getting different answers. Have you tried aligning the predicted protein sequences? Those will likely be more similar than the DNA sequences. And in the end, you probably care most about teh amino acid changes anyway.

[NGS_New_User]

That's a good observation and idea, and it makes sense!
No, I haven't yet tried the predicted protein sequences. I will try that route. Thank you swbarnes2