Phylogenetic or Evolutionary Trees. |
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Gibbs sampling allows the [multiple alignment] of several sequences. It can be turned into simulated annealing to find a (near) optimal multiple alignment. Alternatively, it can statistically sample over many multiple alignments to estimate parameters (branch lengths) and levels of accuracy for these estimates. TransthyretinTransthyretin (Duan et al 1991, Schreiber et al 1992) is a protein expressed in the brain and also expressed in the liver of some animals. There is little doubt about the correct topology of the phylogenetic tree for the six sequences used and the edge estimates (below) were obtained by Gibbs sampling (Allison & Wallace 1994) over 1000 multiple alignments for this tree. The sequences come from
human, sheep, mouse, rat, chicken and reptile (
Bacterial SequencesVarious trees were tried over five and six sequences for chloramphenicol acytyltransferase (CAT) DNA sequences from bacteria (Allison & Wallace 1994). Data
For example: Tree optimal Gibbs (+-SD) ---------------------------------------- ------- ------------ (((CATQ CATB) PC221)((CATP CATD) CCOLI)) 5395 5564(+-36) bits (((CATQ CATB) PC221)((CATP CCOLI) CATD)) 5391 5519(+-32) bits Null: 7752 bitsThere is little to choose between these two trees on the basis of this comparison. References
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