Transition-transversion bias

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Transition-transversion bias
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red -1nt change green - 2nt change blue 3nt change
dark -3st codon pos medium -2nd codon pos light -
1st codon pos
1,889 parameters
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Parsimony vs Maximum likelihood

• Weight matrix C cij - cost of going
• from i to j

• Instantaneous rate matrix Q qij
• leads to equilibrium p
• and transition matrix P pij(t)

-minimum length transformation history below
node a if nucleotide i
-subtree likelihood below node a if nucleotide i
interested in
interested in
parsimoniousness of tree...
likelihood of tree...
to calculate parsimonious nodes...
to calculate nodes given tree...
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rodents, flying lemur, tree shrew, primates
hedgehog, mole, shrew, hedgehog, whales,
ungulates, bats, scaly anteaters, carnivores
armadillo, sloth
elephant, hyrax manatee,aardvark, tenrec
(resemble hedgehog, shrew, opossum, mice, otter)
(1600 highly conserved genes)
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UPGMA

• Dij

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Universal and Eukaryote Phylogenetic Trees.
Structural similarites for 900 sites that can
be unambiguously aligned in a data set of more
than 800 eukaryotes and 100 prokaryotes were
computed and converted to evolutionary distances
using the Kimura two parameter model. The
Neighbor-Joining method was used to infer the
unrooted universal phylogeny shown in A. A
similar computation was used to infer an
unrooted phylogeny in B for diverse eukaryotes
but this analysis is based upon comparisons of
1200 positions that can be unambiguously
aligned. Evolutionary distances in these trees
are proportional to length of line segments
separating taxa.
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http//www.megasoftware.net/
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but not all bacterial DNA is clonally inherited
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http//bacteria.stats.ox.ac.uk