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CATEGORIES:Isaac Newton Institute Seminar Series
SUMMARY:The combinatorics of distance-based tree inference
- Pardi\, F (CNRS)
DTSTART;TZID=Europe/London:20110624T104000
DTEND;TZID=Europe/London:20110624T110000
UID:TALK31880AThttp://talks.cam.ac.uk
URL:http://talks.cam.ac.uk/talk/index/31880
DESCRIPTION:Several popular methods for phylogenetic inference
(or hierarchical clustering) are based on a matri
x of pairwise distances between taxa (or any kind
of objects): the objective is to construct a tree
with branch lengths so that the distances between
the leaves in that tree are as close as possible t
o the input distances. If we hold the structure (t
opology) of the tree fixed\, in some relevant case
s the optimal values for the branch lengths can be
expressed using simple combinatiorial formulae. H
ere we define a general form for these formulae an
d show that they all have two desirable properties
: first\, the common tree reconstruction approache
s (least squares\, minimum evolution)\, when used
in combination with these formulae\, are guarantee
d to infer the correct tree when given enough data
(consistency)\; second\, the branch lengths of al
l the simple (NNI) rearrangements of a tree can be
calculated\, optimally\, in quadratric time in th
e size of the tree. The study presented here may f
orm the basis for novel effcient search algorithms
for distance-based tree reconstruction.\n
LOCATION:Seminar Room 1\, Newton Institute
CONTACT:Mustapha Amrani
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