4 Works

Data from: Understanding angiosperm diversification using small and large phylogenetic trees

Stephen A. Smith, Jeremy M. Beaulieu, Alexandros Stamatakis & Michael J. Donoghue
How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the...

Data from: SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Kevin Liu, Tandy J. Warnow, Mark T. Holder, Serita M. Nelesen, Jiaye Yu, Alexandros P. Stamatakis & C. Randal Linder
Highly accurate estimation of phylogenetic trees for large datasets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Co-estimation of alignments and trees has been attempted, but currently only SATé estimates reasonably accurate trees and alignments for large datasets in practical time frames (Liu et al., 2009b). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I)...

Data from: Understanding angiosperm diversification using small and large phylogenetic trees

Stephen A. Smith, Jeremy M. Beaulieu, Alexandros Stamatakis, Michael J. Donoghue, J. M. Beaulieu, M. J. Donoghue, S. A. Smith & A. Stamatakis
How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the...

Data from: SATé-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Kevin Liu, Tandy J. Warnow, Mark T. Holder, Serita M. Nelesen, Jiaye Yu, Alexandros P. Stamatakis & C. Randal Linder
Highly accurate estimation of phylogenetic trees for large datasets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Co-estimation of alignments and trees has been attempted, but currently only SATé estimates reasonably accurate trees and alignments for large datasets in practical time frames (Liu et al., 2009b). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I)...

Registration Year

  • 2011
    4

Resource Types

  • Dataset
    4

Affiliations

  • Heidelberg Institute for Theoretical Studies
    4
  • University of Kansas
    2
  • The University of Texas at Austin
    2
  • Yale University
    2
  • Brown University
    2