Phylogenetic tree

A phylogenetic tree (also phylogeny or evolutionary tree) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. Unrooted trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred. History The idea of a tree of life arose from ancient notions o

Reconstruction of Large-Scale Phylogenies

Vaibhav Rajan

The evolutionary relationships between organisms or phylogenies are fundamental to biology. They are invaluable as guiding tools to mine, organize and exploit the enormous amounts of biological data in the post-genomic era. The advent of high-throughput sequencing has resulted in whole genome data of many organisms and the need for inferring larger phylogenies ; both have necessitated the development of new methods and models in the field of phylogenetic reconstruction. The work presented in this dissertation contributes to this development. Phylogenies are most often inferred from genomic sequences – DNA or amino acid sequences. A key step before using a phylogenetic reconstruction method is that of aligning the input sequences. Finding accurate multiple sequence alignments is hard because of the heterogeneity of evolutionary signal present in the sequences—a more acute problem in whole genome sequences. A new approach to refining the phylogenetic signal of alignments is presented that identifies and eliminates phylogenetically noisy parts of the alignment in order to yield better phylogenies. The more recent model of evolution based on rearrangements (large-scale structural changes in genomes) has been a major step towards reconstructing large phylogenies. The design of models and methods in this area has presented significant mathematical challenges and some of these algorithmic and statistical questions are addressed in this work. The efficacy of simple distance-based methods are demonstrated in building accurate trees with rearrangement data, using precise estimates of true evolutionary distances. Novel methods methods are designed for robustness assessment of trees inferred by such distance-based methods. These methods are the first methods for robustness assessment for trees inferred from rearrangement data that are on par with previous such measures for trees inferred from sequence data. Further, two algorithmic problems on inversions are discussed : sorting by inversions and the inversion median problem. New algorithms and theoretical insights about the structure of the problems are described.

EPFL2012

FluRF, an automated flu virus reassortment finder based on phylogenetic trees

Bernard Moret, Alisa Yurovsky

Background: Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemics of the last century, their identification has become a health priority. While such identification can be done "by hand" on a small dataset, researchers and health authorities are building up enormous databases of genomic sequences for every flu strain, so that it is imperative to develop automated identification methods. However, current methods are limited to pairwise segment comparisons.

IEEE2010

Reconstruction of Large-Scale Phylogenies

Vaibhav Rajan

EPFL2012

Reconstruction of Large-Scale Phylogenies

FluRF, an automated flu virus reassortment finder based on phylogenetic trees

FluReF, an automated flu virus reassortment finder based on phylogenetic trees

FluReF, an automated flu virus reassortment finder based on phylogenetic trees

Reconstruction of Large-Scale Phylogenies

FluRF, an automated flu virus reassortment finder based on phylogenetic trees