NEED: Tree alignment of Protein sequences

Georg Fuellen fuellen at math10.Mathematik.Uni-Bielefeld.DE
Fri Jul 22 10:45:01 EST 1994


In article <CtArB2.CKH at hermes.hrz.uni-bielefeld.de>, I wrote:
|> Is there any paper featuring a tree alignment of protein sequences ?? 
|> (i.e. an alignment with reconstructed ancestral sequences)
|> All I could dig out so far were tree alignments of RNA sequences 
|> and non-tree multiple alignments.
|> 
|> Of course, an electronically accessible tree alignment would be
|> just marvellous...
|> Or maybe you can email such a thing to me ?

Let me explain what I meant with "tree alignment":

Given a phylogenetic tree, you may calculate a multiple alignment. 
But I need the ancestral sequences be calculated as well, i.e.
the inner nodes of the phylogenetic tree must be labeled as well :

                 root ALWVG   <----------------------------
               /            \
            AL-LL  <-      LLWVG   <-
           /     \        /     \
        AL-LL   GL--L   LLWVG  LL-VG

Now the corresponding __tree alignment__ is

ALWVG (*)   <-----------------------------------------------
AL-LL (*)   <-
LLWVG (*)   <-
AL-LL
GL--L
LLWVG
LL-VG

where "<-" indicates reconstructed sequences. (artificial example)

 
  georg
fuellen at Mathematik.Uni-Bielefeld.DE
fuellen at MIT.EDU
Dr Stephen R Covey, The 7 Habits of Highly Effective People, Habit #4:
THINK WIN/WIN !                                                  





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