Phylogenetic or Evolutionary Trees.

home
 Bib
 Algorithms
 Bioinfo
 FP
 Logic
 MML
 Prog.Lang
and the
 mmlist

Bioinf
 Notes
  trees
  more

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.

Transthyretin

Transthyretin (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.

Phylogenetic Tree for 
Transthyretin DNA sequences

The sequences come from human, sheep, mouse, rat, chicken and reptile (T. rugosa).

Data:
HUMPALA (27-470)
OATTHYRE (12-452)
MMALBR (27-467)
RATPALTA (10-453)
GDTRTHY (26-478)
TRTRANST (16-468)

Bacterial Sequences

Various trees were tried over five and six sequences for chloramphenicol acytyltransferase (CAT) DNA sequences from bacteria (Allison & Wallace 1994).

Evolutionary Tree for six Bacterial DNA sequences

Data

CATQ m55620 Clostridium Perfringens 459-1118
CATP m28717 Clostridium Perfringens 145-768
CATD x15100 Clostridium Difficile 91-726
CCOLI m35190 Campylobacter Coli 309-932
CATB m93113 Clostridium Butyricum 145-800
PC221 spc221 Staphylococus Aureus 2267-2914

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 bits
There is little to choose between these two trees on the basis of this comparison.

References

  • L. Allison & C. S. Wallace. The Posterior Probability Distribution of Alignments and its Application to Parameter Estimation of Evolutionary Trees and to Optimization of Multiple Alignments. Jrnl. Mol. Evol. 39 418-430 1994 [HTML].
  • W. Duan, M. G. Achen, S. J. Richardson, M. C. Lawrence, R. E. H. Wettenhall, A. Jaworowski, G. Schreiber. Isolation, Characterisation, cDNA Cloning and Gene Expression of an Avian Transthyretin: Implications for the Evolution of Structure and Function of Transthyretin in Vertebrates. Eur. J. Biochem. 200 679-687 1991.
  • A. S. Huggins, T. L. Bannam, J. I. Rood. Comparative Sequence Analysis of the catB Gene from Clostridium Butyricum. Chemother. 36(11) 2548-2551 1992.
  • G. Shrieber, A. R. Aldred, W. Duan. Choroid Plexus, Brain Protein-Homeostasis and Evolution. Today's Life Science, Sept., 22-28 1992.
Coding Ockham's Razor, L. Allison, Springer

A Practical Introduction to Denotational Semantics, L. Allison, CUP

Linux
 Ubuntu
free op. sys.
OpenOffice
free office suite
The GIMP
~ free photoshop
Firefox
web browser

© L. Allison   http://www.allisons.org/ll/   (or as otherwise indicated),
Faculty of Information Technology (Clayton), Monash University, Australia 3800 (6/'05 was School of Computer Science and Software Engineering, Fac. Info. Tech., Monash University,
was Department of Computer Science, Fac. Comp. & Info. Tech., '89 was Department of Computer Science, Fac. Sci., '68-'71 was Department of Information Science, Fac. Sci.)
Created with "vi (Linux + Solaris)",  charset=iso-8859-1,  fetched Saturday, 21-May-2022 09:24:06 AEST.