an introduction

David Bryant

Description

Supertrees (an introduction) David Bryant McGill Centre for Bioinformatics Montréal, Québec

• containing overlapping


• trees can


• consensus method


• rooted tree


• labelled leaves


• trees


• mcgill centre

Sujets

• Bryant
• Gordon
• Tree (graph theory)

Informations

• Publié par: pefav
• Nombre de lectures: 7
• Langue: English
• Poids de l'ouvrage: 9 Mo

Extrait

Supertreess
(an introduction)
David Bryanntt
McGill Centre for Bioinformatics
Montréal, QuébecEdward N. Adams III (1972):
A new problem in the science of classification is
presented, along with its solution.
The problem is to combine the information in several
taxonomic trees into a single tree. The solution is a
computational method for computing a tree which
represents only that information shared by the rival
trees.
Such a method is called the consensus method.Consensus Trees
Consensus tree
Consensus method
Input treesAllan Gordon (1986)
Consensus Supertrees: the synthesis of rooted trees
containing overlapping sets of labelled leaves.
A supertree is a dendrogram [rooted tree] from which
each of the original trees can be regarded as samples.Supertrees
Supertree method
Supertree
Input treesAn introduction to Supertrees
1. What is a supertree method?
2. Why supertrees?
3. A taste of supertree mathematics
4. A tour of supertree methods
5. ReservationsAn introduction to Supertrees
1. What is a supertree method?
2. Why supertrees?
3. A taste of supertree mathematics
4. A tour of supertree methods
5. ReservationsWhy supertrees? Goals
The quest for the best supertree is complicated by the fact
that there are several quite different goals in supertree
construction.
a) Assist optimisation
b) Compare, contrast, collate
c) Uncover hidden phylogenetic
information
d) Analyse heterogeneous data(a) Optimisation
• Supertrees can help find the tree(s) optimizing some
objective criterion.
•Divide and conquer is one of the oldest (and most
effective) strategies in computer science.
• Three steps:
v Divide sequences in smaller groups
v Analyse each group separately
v Combine analyses into a supertree
• Can give dramatic reductions in computing time(b) Compare - contrast -
collate
• The oldest `supertree’ approach
• Exponentially growing number of
phylogenetic studies
• Need to understand
1. Wider relationships
2. Interesting conflicts
3. Poorly sampled groups
• e.g. mammal study of Liu et al. (315
articles)