Documente Academic
Documente Profesional
Documente Cultură
Tbingen, Germany
University, Ramat-Gan, Israel
3 International Computer Science Institute, Berkeley, USA
4 Tel-Aviv University, Israel
5 Universitt zu Lbeck, Germany
2 Bar-Ilan
Outline
Solutions:
Additional assumption like the rich data hypothesis.
2
Solutions:
Look for phylogenetic networks.
Correct data.
Find blocks where a perfect phylogeny is possible.
no perfect phylogeny
perfect phylogeny
perfect phylogeny
perfect phylogeny
perfect phylogeny
perfect phylogeny
perfect phylogeny
no perfect phylogeny
M:
0
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
0
0
0
0
0
0
0
0
0
1
1
1
0
0
0
0
1
0
0
0
M:
0
0
1
0
1
0
1
0
1
0
1
0
1
0
1
1
0
0
0
0
0
0
0
0
0
1
1
1
0
0
0
0
1
0
0
0
Perfect phylogeny
Perfect phylogeny
PP (M) = 2.
Let G be a graph.
0
0
1
1
0
1
0
1
Corollary
If PP (M) = 2 for a haplotype matrix M, we can find an optimal
pp-partition in polynomial time.
Corollary
Computing PP for haplotype matrices is
NP-hard,
not fixed-parameter tractable, unless P = NP,
very hard to approximate.
M:
2
1
0
0
0
1
2
0
0
0
2
1
2
0
0
1
2
0
2
0
1
0
0
0
M:
2
1
0
0
0
1
2
0
0
0
2
1
2
0
0
1
2
0
2
0
1
0
0
0
Perfect phylogeny
Perfect phylogeny
PP (M) = 2.
2
1
0
0
2
0
1
0
2
0
0
1
Corollary
Even if we know PP (M) = 2 for a genotype matrix M,
finding a pp-partition of any fixed size is still
NP-hard,
not fixed-parameter tractable, unless P = NP,
very hard to approximate.
Genotype matrix
G:
A
2
0
2
0
B
2
2
0
2
C
2
0
0
2
Haplotype matrix
H:
A
1
0
0
0
0
1
0
0
B
0
1
0
1
0
0
0
1
C
0
1
0
0
0
0
0
1
Summary
Genotype matrix
G:
A
2
0
1
0
B
2
1
0
2
C
2
2
0
2
D
2
1
1
0
Partial order
E
2
0
2
0
Partial order:
Genotype matrix
G:
A
2
0
1
0
B
2
1
0
2
C
2
2
0
2
D
2
1
1
0
Partial order
E
2
0
2
0
Partial order:
Compatible as children of root:
Partial order
D
Matching graph
D0
A0
B0
E0
C0
Return
Partial order
D
Matching graph
D0
A0
B0
E0
C0
Partial order
D
Matching graph
D0
A0
B0
E0
C0