I have two protein sequences with around 50% identity between them.
I want to study the phylogenetic relationship between them.
I came up with a method myself:
Step 1: blast each of the sequences to a protein database separately (possibly with less stringent thresholds)
Step 2: extract the subject sequences which are hits common to both blasts
Step 3: multiple sequence alignment using the common subject seqeunces and the two query sequences
Step 4: build the phylogenetic tree
Could anyone comment on this method? If it is not ideal, what is the standard way of preparing homolog sequences for a phylogenetic analysis?
Thank you.
Here is an Practical Approach to phylogenetic analysis and hypothesis testing: https://www.kuleuven.be/aidslab/phylogenybook/home.html
www.cmore.soest.hawaii.edu/education/grads.../arb.../Tutorial_3_phylogenetic%20trees.doc
It depends on what type of protein, what type of organisms they are from, and what you would like to learn about the proteins. Studying members of a large family such as serine/threonine kinases in mammals is quite different from studying viral RNA polymerases.
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