Publications related to Phylogenetic comparative methods

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, ...

Oxford University Press2012

Comparing COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida)

Edward Mitchell, Enrique Lara, Thierry Jean Heger

The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal “DNA barcode” for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses h ...

2011

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Yu Lin, Vaibhav Rajan

Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed ...

Springer Verlag2011

A metric for phylogenetic trees based on matching

Bernard Moret, Yu Lin, Vaibhav Rajan

Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so t ...

Springer Verlag2011

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Bernard Moret, Yu Lin, Vaibhav Rajan

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...

2011

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

Sebastian Maerkl

Transcription factor binding site(s) (TFBS) gain and loss (i.e., turnover) is a well-documented feature of cis-regulatory module (CRM) evolution, yet little attention has been paid to the evolutionary force(s) driving this turnover process. The predominant ...

Public Library of Science2011

Numerical Ecology with R

François Gillet, Daniel Borcard

Numerical Ecology with R provides a long-awaited bridge between a textbook in Numerical Ecology and the implementation of this discipline in the R language. After short theoretical overviews, the authors accompany the users through the exploration of the m ...

Springer2011

Inferring transcript phylogenies

Bernard Moret, Yann Christinat

Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals - some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite ...

IEEE Press2011

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Phylogenetic comparative methods

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

Transcriptional Regulatory Networks across Species

Comparing COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida)

Bootstrapping phylogenies inferred from rearrangement data

A metric for phylogenetic trees based on matching

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

Numerical Ecology with R

Inferring transcript phylogenies

On Exploring Genome Rearrangement Phylogenetic Patterns

Graph Chatbot

Chat with Graph Search

Comparing COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida)

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

Inferring transcript phylogenies

Transcriptional Regulatory Networks across Species

A metric for phylogenetic trees based on matching

Bootstrapping phylogenies inferred from rearrangement data

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

On Exploring Genome Rearrangement Phylogenetic Patterns

Numerical Ecology with R