lamoran at gpu.utcs.utoronto.ca (L.A. Moran) writes:
: 3. align amino acid residues manually using a word processor
: 4. convert to nucleotide alignment by codons
: 5. derive a consensus manually taking into account the phylogenetic
: distance between species and ignoring biases such as a large number
: of genes from closely related organisms
:: In my opinion it is wrong to assume that any computer program can do a
: better job than an intelligent human when it comes to multiple sequence
: alignments and deriving a consensus.
:
I can't let this one go by without a comment...
When you are dealing with very conserved sequences, the human eye (brain) can
align sequences pretty well, but when dealing with more distant relationships,
the computer is a really big help.
Thus, I would suggest using a multiple alignment program on some system (I
don't know of one that runs on the mac and is PD/shareware), and then OPTIMIZE
the alignment manually. I will agree that most (the ones I have used)
multiple alignment programs don't align sequences exactly the way I would
like, but it is usually fairly easy to edit what they give you to end up with
a very good alignment.
Also... doesn't PIMA work with coding sequences when aligning proteins, or
something like that? Anyone know?
Also*2... for doing phylogenetic analyses on the MAc, PAUP, written by David
Swofford and available for about $50, is a great program.
Later,
Keith
--
Keith O. Elliston elliston at msdrl.com uunet!av8tr!elliston
AA5A/U N9734U elliston at mbcl.rutgers.eduelliston at biovax.bitnet
"Beware of pseudo-experts with a mission and a grudge, especially if they are
lawyers pretending to be scientists." -- H.W. Lewis in 'Technological Risk'
