Note: this question has also been asked on Biostars

This is question regarding the tools rather than the concepts.

I am a freshman at college and I am a working on an evolutionary biology of eukaryotic cells project. I have come across two different sets of methods in the papers I read. One is BLAST and one is eggNOG. From what I have learnt BLAST is basically used to find segments of matches between the query an the source by using W substrings of nucleotides, expanding their neighborhood up to some set limit and then searching in a hashed database. I have not come across eggNOG before. The Wikipedia page says it is maintained by EMBL and has clusters of orthologous groups. Besides this I have no information about the differences in the two. I also plan to use Hidden Markov Models during genome alignment and I shall eventually be using this information to construct phylogenetic trees to infer changes.

Could someone please help me out by telling the differences between the two ? And would using HMMs really make a difference ? I would be implementing the HMMs from scratch mostly as I have not found tools that do that like BLAST or eggNOG.

I am currently learning relevant parts of computational biology from an online course so this is the reason that I have this doubt. I would be very grateful for any help that you could provide.

I had asked this on the bio stack exchange and I was told that this is the appropriate SE for this question.


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