Molecular tools for phylogenetics at different scales: From phylogeography to supertrees

On building and comparing trees Application to supertrees in phylogenetics

5 te l-0 03 60 92 6, v er si on 1 12 F eb 2 00 9 The research work presented in this manuscript is of algorithmic kind: it is mainly composed of polynomial, fixed parameter and approximation algorithms, while hardness results are also mentioned. This work is about building and comparing labelled trees. These objects find application in different areas, but notoriously in phylogenetics, where th...

DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics, and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-med...

Modeling plant morphogenesis at different scales, from genes to phenotype

Applications of next-generation sequencing to phylogeography and phylogenetics.

This is a time of unprecedented transition in DNA sequencing technologies. Next-generation sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus sequence data for phylogeography and phylogenetics. However, the focus on non-model organisms, in addition to uncertainty about which sample preparation methods and analyses are appropriate for different research q...

Reticulation, divergence, and the phylogeography-phylogenetics continuum.

Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombi...