Does exists a sequence error correction software that uses a MSA result to resolve read errors at specific SNP positions?

Question

[andreagarcia871]

I have an input DNA sequence with read errors (bases appear as [A/G] for example). I have also a multiple sequence alignment of all current alleles reported for a gene in a specific region of interest.

Now I want to find which combination of alleles in the MSA explains the combination of polymorphisms in my input sequence. Is there a software or reported algorithm for such task?

Answer 1

[Soumitra Pal]

Are you looking for some error correction software like CORAL?
http://www.ncbi.nlm.nih.gov/pubmed/21471014