Hello, could anyone suggest me an alignment editor program that generates a reliable consensus sequence out the MSA? I tried a number of such programs (Bioedit, Jalview, Seaview etc.). Problem: there is option to change the parameters (threshold values) however, the length of consensus sequence is different while changing the parameters. It can be best explained by the image below. For me, the program should generate the consensus with equal length by ignoring obviously underrepresented positions.
Thanks in advance