Literature DB >> 21933452

Inferring the Tree of Life: chopping a phylogenomic problem down to size?

Olaf R P Bininda-Emonds1.   

Abstract

The combination of molecular sequence data and bioinformatics has revolutionized phylogenetic inference over the past decade, vastly increasing the scope of the evolutionary trees that we are able to infer. A recent paper in BMC Biology describing a new phylogenomic pipeline to help automate the inference of evolutionary trees from public sequence databases provides another important tool in our efforts to derive the Tree of Life.

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Mesh:

Year:  2011        PMID: 21933452      PMCID: PMC3176480          DOI: 10.1186/1741-7007-9-59

Source DB:  PubMed          Journal:  BMC Biol        ISSN: 1741-7007            Impact factor:   7.431


  10 in total

Review 1.  Unanswered questions in ecology.

Authors:  R May
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1999-12-29       Impact factor: 6.237

Review 2.  The challenge of constructing large phylogenetic trees.

Authors:  Michael J Sanderson; Amy C Driskell
Journal:  Trends Plant Sci       Date:  2003-08       Impact factor: 18.313

3.  Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom-forming fungi).

Authors:  David S Hibbett; R Henrik Nilsson; Marc Snyder; Mario Fonseca; Janine Costanzo; Moran Shonfeld
Journal:  Syst Biol       Date:  2005-08       Impact factor: 15.683

4.  A phylogenomic analysis of the Ascomycota.

Authors:  Barbara Robbertse; John B Reeves; Conrad L Schoch; Joseph W Spatafora
Journal:  Fungal Genet Biol       Date:  2006-06-15       Impact factor: 3.495

5.  Toward automatic reconstruction of a highly resolved tree of life.

Authors:  Francesca D Ciccarelli; Tobias Doerks; Christian von Mering; Christopher J Creevey; Berend Snel; Peer Bork
Journal:  Science       Date:  2006-03-03       Impact factor: 47.728

6.  Preserving accuracy in GenBank.

Authors:  M I Bidartondo
Journal:  Science       Date:  2008-03-21       Impact factor: 47.728

Review 7.  Understanding angiosperm diversification using small and large phylogenetic trees.

Authors:  Stephen A Smith; Jeremy M Beaulieu; Alexandros Stamatakis; Michael J Donoghue
Journal:  Am J Bot       Date:  2011-03-02       Impact factor: 3.844

8.  Comparisons between mitochondrial genomes of domestic goat (Capra hircus) reveal the presence of numts and multiple sequencing errors.

Authors:  Alexandre Hassanin; Céline Bonillo; Bui Xuan Nguyen; Corinne Cruaud
Journal:  Mitochondrial DNA       Date:  2010-06

9.  The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences.

Authors:  Ralph S Peters; Benjamin Meyer; Lars Krogmann; Janus Borner; Karen Meusemann; Kai Schütte; Oliver Niehuis; Bernhard Misof
Journal:  BMC Biol       Date:  2011-08-18       Impact factor: 7.431

10.  An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).

Authors:  Dongying Wu; Amber Hartman; Naomi Ward; Jonathan A Eisen
Journal:  PLoS One       Date:  2008-07-02       Impact factor: 3.240

  10 in total
  1 in total

1.  A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.

Authors:  Leonardo De Oliveira Martins; Diego Mallo; David Posada
Journal:  Syst Biol       Date:  2014-10-03       Impact factor: 15.683

  1 in total

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