title: Stability analysis of phylogenetic trees.
abstract: BACKGROUND
  Phylogenetics, or reconstructing the evolutionary relationships of organisms, is critical for understanding evolution. A large number of heuristic algorithms for phylogenetics have been developed, some of which enable estimates of trees with tens of thousands of taxa. Such trees may not be robust, as small changes in the input data can cause major differences in the optimal topology. Tools that can assess the quality and stability of phylogenetic tree estimates and identify the most reliable parts of the tree are needed.
  
  
  RESULTS
  We define measures that assess the stability of trees, subtrees and individual taxa with respect to changes in the input sequences. Our measures consider changes at the finest granularity in the input data (i.e. individual nucleotides). We demonstrate the effectiveness of our measures on large published datasets. Our measures are computationally feasible for phylogenetic datasets consisting of tens of thousands of taxa.
  
  
  BACKGROUND
  This software is available at http://bioinformatics.cise.ufl.edu/phylostab
  
  
  BACKGROUND
  sheikh@cise.ufl.edu
authors.affiliation: Department of Computer and Information Science and Engineering, University of Florida, FL 32611, USA. sheikh@cise.ufl.edu
authors.forename: Saad I
authors.initials: SI
authors.lastname: Sheikh
authors.forename: Tamer
authors.initials: T
authors.lastname: Kahveci
authors.forename: Sanjay
authors.initials: S
authors.lastname: Ranka
authors.forename: J
authors.initials: J
authors.lastname: Gordon Burleigh
mesh_terms: D000465:Algorithms; D000818:Animals; D008322:Mammals / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software