2 Works

Data from: An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees

Andre J. Aberer, Alexandros Stamatakis & Fredrik Ronquist
Sampling tree space is the most challenging aspect of Bayesian phylogenetic inference. The sheer number of alternative topologies is problematic by itself. In addition, the complex dependency between branch lengths and topology increases the difficulty of moving efficiently among topologies. Current tree proposals are fast but sample new trees using primitive transformations or re-mappings of old branch lengths. This reduces acceptance rates and presumably slows down convergence and mixing. Here, we explore branch proposals that...

Data from: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

Adam D. Leaché, Barbara L. Banbury, Joseph Felsenstein, Adrián Nieto-Montes De Oca & Alexandros Stamatakis
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD...

Registration Year

  • 2015
    2

Resource Types

  • Dataset
    2

Affiliations

  • Heidelberg Institute for Theoretical Studies
    2
  • CIUDAD
    1
  • University of Washington
    1
  • Swedish Museum of Natural History
    1