Hello,
i was trying to alignning multiple sequence with MEGA for constructing phylogenetic tree. after aligning, I am supposed to trimming sequence to make them share equal length.
But i found that cutting tail part then do alignning again, the results would be different. for example, the nucleotide of sequence A was settled in a little ahead after first alignment, but it would settle to a little behind after trimming and alignning again, not as the same position as the first alignment.
I was wondering should sequence align everytime after trimming a part, or just align for the first time
You can trim the unalienable position of both ends within the tool, MEGA. Export it in .aln format or Mega compatible format to generate phylogenetic tree.
By viewing your electropherogram using any software (Chromas, BioEdit, MEGA) you can clean the low-quality parts (often beginning and end), or do a preliminary alignment gainst reference sequence and discard mismatching extremities. After that, you can compute your alignment and dress up your tree using good and representative reference sequences. Don't pay attention to the nucleotide positions, they will change after trimming.
Trim the chromatograms first to remove low quality data, then align. Then choose the region for your tree.
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