Greetings to all,

I have a protein sequence that I got out of BLAST searches and have subjected it to the various motifs scan and have determined it to belong to a class of conserved bacterial proteins.

I need to determine it's phylogenetic relationship with the rest of the bacterial kingdom (including the Archaea) to see where it stands or stick out but there is so many phylogenetic programs with different algorithms like Distance, Parsimony and Maximum Likelihood how do I know what to use and are the results so-called "good experimental data"?

Thanks in advance

You should read the book "Phylogenetic Trees Made Easy" by Barry G. Hall (2nd ed.).
It is simple and comprehensive. Read the complicated ones AFTER this one.

hai!
go to the clustal W site(www.ebi.ac.uk/clustalw/), there u'll find an option for viewing cladogram or phylogram of yur input sequence .
It 'll be the easiest.