I look for nucleotide sequence alignment tools similar as SeqMan (DNAstar). Indeed, I am using Needle in a Linux terminal which I found very helpful, but results between the two softwares are different and I'm trying to understand why..
Do you know what matrix is used by SeqMan? For Needle, I use the EDNAFULL matrix.
The main differences are coming from heterogenicity in base calls during sequencing (R = A,G, Y = C, T, etc.), when compared to a reference sequence that only contains A, T, G and C nucleotides. Similarity percentages are equivalent between Needle and SeqMan but identity percentages (that take into consideration base heterogenicity) are different.
Thank you very much for your appreciated help!