I want to do a Phylogenetic analysis to classify organisms using following sequences.
I have download some sequences (ITS region) from NCBI database and aligned them but because of few sequences long gaps have been generated see picture.
My question is what to do with these kind of sequences? Can i remove the middle portion of these sequences to reduce gap or i should just leave it like that. Can i exclude those sequences from my studies because of these long gaps??
I don't think there is a single answer to that as it will depend on what question(s) you are trying to answer. I would not generally discard a single sequence just because it has inserts others dont. Also, this alignment just does not look very homologous (ie from bases 180-210), so maybe these sequences just cannot be aligned well (can also try different algorithms or settings). If in doubt you can go back to the original article and see if this particular sequence was unique in any way.
What is the aim behind generating the phylogenetic tree? Are u looking for common domains? Are you looking to classify the organisms?
Depending on your objective your blast parameters would change. What if you compare the proteins? As I said without having a clear idea on the aim of this multiple alignment I can not provide a concrete answer.
If the organisms are very close to each other DNA sequence is better since it can reveal the subtle variations that exist between them however if the organisms are some how far then the usage of proteins sequences is better. Honestly I always used proteins sequences (for the few analysis I did in this aspect). Try to use the curated one.
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