HI ALL I need to analyze few whole genome sequences of phages . In order for me to do that i need to have the same start point for all these phages. Right now lot of these phages are quite similar but they have different start points hence im not able to to see the mutations. I have done multiple genome alignments using clustal omega but i see a lot of gaps in these phages which i assume is because they are not aligned properly. how to arrange them so that they all have the same start point?