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Phylogenetics Virtual Issue

The reconstruction of reliable phylogenetic trees is essential for depicting and understanding the diversity of life. The unprecedented amount of genomic data from model and nonmodel organisms resulting from next-generation sequencing techniques has opened a new era in phylogenomics, paving the way toward the resolution of difficult and complex phylogenetic problems in the Tree of Life. Indeed, main milestones in this road will be the development of accurate statistical methods that take into account the complexities of this type of data and their implementation in efficient computational tools.

In this virtual issue we pretend to gather a set of papers that explore potential solutions to common problems in statistical and computational phylogenomics, like improved models of molecular evolution, estimation from large data, gene tree and species tree incongruence, including lineage sorting, gene duplication and loss, and horizontal gene transfer, and others.

Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency

Guy Baele and Philippe Lemey
Bioinformatics (2013), Volume 29, Issue 16, 1970-1979; doi: 10.1093/bioinformatics/btt340
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Naive binning improves phylogenomic analyses

Md Shamsuzzoha Bayzid and Tandy Warnow
Bioinformatics (2013), Volume 29, Issue 18, 2277-2284; doi: 10.1093/bioinformatics/btt394
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A general species delimitation method with applications to phylogenetic placements

Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis and Alexandros Stamatakis
Bioinformatics (2013), Volume 29, Issue 22, 2869-2876; doi: 10.1093/bioinformatics/btt499
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