After sequencing when a set of data was fed in MEGA for Alignment (CLUSTAL W or MUSCLE), I found a huge gap in between the sequences (middle portion), should that also be pruned or left as such? Will that affect my tree topology and lead to least Bootstrap value Or PP value?
Your question does not provide any information of what the sequences are and how are they processed.
Please go through some basic lectures/literature about molecular biology and sequence data analysis to make things easier.
Are you processing sequences of the same species or different? If you are working with different species then the gaps are common issue and you should process without trimming those gaps but if you are working with sequences of a same species then you should check your sequence quality.
I am just a beginner in this field. I had used single marker (rbcl) for different species. Found some sequence gap in middle. Just wanted to know the reason. Thanks for the suggestions and reply.
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