What I would like to to is to generate a phylogenetic tree based on 16s
sequences from 30 different bacteria plotted onto a larger tree showing
selected organisms from different prominent phyla. The idea is to
display the relationship between my 30 organisms AND how they relate to
the rest of the prokaryotes.
I used to this sort of thing by downloading each sequence from NCBI and
then align them and generate a phylogenetic tree in ClustalW or some
other software. I hope there exist some internet tools now that can do
it all for me, i.e. that I just select the species/strains and the
software retrives the sequences, aligns them and creates the tree
according to mye criteria. Do you know of any such sequences or do
people still do these kind of things "by hand"?