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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Distorted metrics on trees and phylogenetic forests.

Elchanan Mossel¹

¹Department of Statistics, University of California at Berkeley, 94720-3860, USA. mossel@stat.berkeley.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|February 6, 2007

Summary

This study introduces a method to reconstruct phylogenetic trees even with distorted distance data. It enables efficient reconstruction of evolutionary relationships from limited sequence information.

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Area of Science:

Computational Biology
Phylogenetics
Graph Theory

Background:

Phylogenetic reconstruction relies on accurate distance metrics between species.
Distorted metrics can arise from various biological processes, complicating tree building.
Existing methods struggle with significant metric distortions.

Purpose of the Study:

To develop a method for reconstructing binary trees from distorted path metrics.
To establish theoretical bounds on the number of trees in the reconstructed forest.
To enable efficient phylogenetic forest reconstruction from limited sequence data.

Main Methods:

Analysis of distorted metrics on binary trees, defining distortion bounds.
Development of a polynomial-time algorithm to reconstruct a forest of trees.
Application of the distorted metric result to phylogenetic reconstruction under the general Markov model.

Main Results:

A polynomial-time algorithm reconstructs a forest (T1,...,Talpha) from distorted metrics.
The number of trees in the forest (alpha - 1) is bounded by 2(-omega(M/g))n.
This implies a reconstruction algorithm for phylogenetic forests from logarithmic sequence lengths.

Conclusions:

Distorted metrics can be effectively handled in phylogenetic reconstruction.
The developed method allows for efficient reconstruction of evolutionary histories.
The theoretical results are nearly tight, indicating the efficiency of the approach.