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Introduction VETO methods with desirable proprieties

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1/ 29 Introduction VETO methods with desirable proprieties STC preprocess PhySIC IST : cleaning source trees to infer more informative supertrees. Celine Scornavacca, Vincent Berry, Vincent Ranwez et Emmanuel J.P. Douzery LIRMM, UMR CNRS 5506 ISEM, UMR CNRS 5554 University of Montpellier II June 16, 2008 Celine Scornavacca PhySIC IST

  • supermatrix approach

  • source datasets

  • introduction veto

  • vote methods

  • assembling datasets

  • stc preprocess

  • cleaning source

  • physic ist


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Introduction
VETO methods with desirable proprieties
STC preprocess
PhySIC IST: cleaning source trees to infer more
informative supertrees.
Celine Scornavacca,
Vincent Berry,
Vincent Ranwez et Emmanuel J.P. Douzery
LIRMM, UMR CNRS 5506
ISEM, UMR CNRS 5554
University of Montpellier II
June 16, 2008
1/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Reconstruction of phylogenies
Input: (different) source datasets
2/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Reconstruction of phylogenies
Input: (different) source datasets
output: A large phylogeny
2/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Reconstruction of phylogenies for multiple datasets
Two main approaches
Supermatrix approach: assembling datasets
3/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Reconstruction of phylogenies for multiple datasets
Two main approaches
Supermatrix approach: assembling datasets
Supertree approach: assembling trees
3/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Interest of supertrees
Supertrees are useful for:
Combining heterogeneous data
Obtaining a phylogeny using several genes:
◮ Avoids having to deal with too much missing data
◮ Evolutionary models adapted for each gene sequence
Pointing out problematic areas of the phylogeny
◮ agreement and disagreement among input trees.
◮ measuring taxon overlap
4/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Supertree methods
VOTE vs VETO methods
Supertree methods can be classified into two categories, depending on the
way they deal with incongruent data:
5/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Supertree methods
VOTE vs VETO methods
Supertree methods can be classified into two categories, depending on the
way they deal with incongruent data:
Vote methods resolve conflicts, opting for the resolution that
maximizes their optimization criteria.
worrying feature: this approach can lead to propose clades
contradicting all source trees.
T1 T2 T3
A A B A
B B A B
C C C C
E E E E
F F F
5/ 29
Celine Scornavacca PhySIC ISTIntroduction Combining data for phylogenetic inferences
VETO methods with desirable proprieties Vote methods
STC preprocess Veto methods
Supertree methods
VOTE vs VETO methods
Veto methods do not allow the resulting supertree to contain clades
that a source tree would vote against.
◮ pruning some taxa:
OR
◮ proposing multifurcations
worrying feature: this approach can lead to propose unresolved
supertrees.
T1 T2 T3
A A B A
B B A B
C C C C
E E E E
F F F
6/ 29
Celine Scornavacca PhySIC ISTIntroduction
Physic
VETO methods with desirable proprieties
PhySIC IST
STC preprocess
PhySIC
A VETO method with desirable proprieties
The resulting supertree does not contain relationships contradicting
the source trees (non-contradiction property, denoted by PC);
7/ 29
Celine Scornavacca PhySIC IST

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