[Popgenlunch] Seminar on Thursday the 10th at 12:30 by Shlomo Moran on the Adaptive Distances method

Joe Felsenstein joe at gs.washington.edu
Thu Sep 3 15:16:56 PDT 2015

(please spread this announcement to other relevant mailing lists)

Folks --

Shlomo Moran, who is Professor in the Department of Computer Science
at the Technion in Haifa, Israel, will be visiting Seattle next week.
He has agreed to give a seminar:

On Thursday, September 10

from 12:30 - 1:30pm

in S110 Foege Building


The adaptive distances method in evolutionary models

He has provided this abstract:

Evolutionary distances between pairs of aligned DNA sequences
(representing species or genes) are very useful for reconstructing
phylogenetic (evolutionary) trees. Obtaining good estimations of
these distances is critical for accurate tree reconstruction.
Traditionally, evolutionary distances are identified with evolutionary
time - the expected number of substitutions (mutations) per site,
which is estimated from the aligned sequences and the assumed
evolutionary model. When different types of substitutions (e.g.,
transitions and transversions) occur at different rates, then
estimates of their counts have different statistical properties; due
to the finite length of the aligned sequences, it is hard to estimate
the expected number of fast substitutions types when the sequences are
(time-wise) far apart - a phenomenon known as "site saturation". It
is similarly hard to estimate the expected number of slow
substitutions types when these sequences are close. This suggests that
for estimating long distances we should use a distance function which
is based on slow mutation types, and for estimating small distances we
should use a distance function which is based on fast mutation types.
This is what the adaptive distances method aims at. I will present
the algebraic properties of the evolutionary models which enable the
use of adaptive distances, and then report theoretical and
experimental results which demonstrate the advantages of this method.
Time permitting, some related extensions and applications of this
method will be presented.

The talk is based on the following papers:

Gronau, I., S. Moran, and I. Yavneh. 2009. Towards optimal distance
functions for stochastic substitution models. Journal of Theoretical
Biology 260 (2): 294-307 (main part of the talk).

Gronau, I., S. Moran, and I. Yavneh. 2010. Adaptive distance
measures for resolving K2P quartets: Metric separation versus
stochastic noise. Journal of Computational Biology 17 (11):

Doerr, D., I. Gronau, S. Moran, and I. Yavneh. 2012. Stochastic
errors vs. modeling errors in distance based phylogenetic
reconstruction. Algorithms in Molecular Biology 7: 22 (special
issue of invited papers from WABI 2011)

Damti, Y., I. Gronau, S. Moran, and I. Yavneh. 2015. Comparing two
distances. In preparation.

His web site is at: http://www.cs.technion.ac.il/~moran/

He will be around that day and is available to meet with interested
people. I am coordinating his schedule, so please email me to book an

Joe Felsenstein joe at gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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