What do you mean by what should be done? What is your purpose?
But one can't actually do anything with it. If there are gaps, there will be gaps.
Abhijeet Singh Sir first I want to construct a phylogenetic tree from the desired sequences and then from that data a time tree, which is my ultimate goal. When I am aligning my sequences in mega X using muscle alignment a large number of gaps are arising in between those . As you said that one can't do anything with the gaps, then sir should I just draw that tree without trimming?
Aditya Sarkar
As you can see the gaps in alignment are not just gaps, they are also information. Gaps are caused because in some sequences there is something while in others that information is missing which is also a sort of information.
But it is always a debate, whether to trim or not trim an alignment. But in case of trimming, definitely no manual trimming. One can try programs like trimAl or GBlocks for the purpose.
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