PMID- 20584772
OWN - NLM
STAT- MEDLINE
DCOM- 20110228
LR  - 20101115
IS  - 1537-1719 (Electronic)
IS  - 0737-4038 (Linking)
VI  - 27
IP  - 12
DP  - 2010 Dec
TI  - The prevalence of multifurcations in tree-space and their implications for 
      tree-search.
PG  - 2674-7
LID - 10.1093/molbev/msq163 [doi]
AB  - Phylogenetic tree-search is a major aspect of many evolutionary studies. Several 
      tree rearrangement algorithms are available for tree-search, but it is hard to 
      draw general conclusions about their relative performance because many effects 
      are data set specific and can be highly dependent on individual implementations 
      (e.g., RAxML or phyml). Using only the structure of the rearrangements proposed 
      by the Nearest Neighbor Interchange (NNI) algorithm, we show tree-search can 
      prematurely terminate if it encounters multifurcating trees. We validate the 
      relevance of this result by demonstrating that in real data the majority of 
      possible bifurcating trees potentially encountered during tree-search are 
      actually multifurcations, which suggests NNI would be expected to perform poorly. 
      We also show that the star-decomposition algorithm is a special case of two other 
      popular tree-search algorithms, subtree pruning and regrafting (SPR) and tree 
      bisection and reconnection (TBR), which means that these two algorithms can 
      efficiently escape when they encounter multifurcations. We caution against the 
      use of the NNI algorithm and for most applications we recommend the use of more 
      robust tree-search algorithms, such as SPR and TBR.
FAU - Whelan, Simon
AU  - Whelan S
FAU - Money, Daniel
AU  - Money D
LA  - eng
PT  - Letter
PT  - Research Support, Non-U.S. Gov't
DEP - 20100628
PL  - United States
TA  - Mol Biol Evol
JT  - Molecular biology and evolution
JID - 8501455
SB  - IM
MH  - Algorithms
MH  - *Evolution, Molecular
MH  - Likelihood Functions
MH  - *Models, Genetic
MH  - *Phylogeny
MH  - Sequence Alignment/*statistics & numerical data
EDAT- 2010/06/30 06:00
MHDA- 2011/03/01 06:00
CRDT- 2010/06/30 06:00
PHST- 2010/06/30 06:00 [entrez]
PHST- 2010/06/30 06:00 [pubmed]
PHST- 2011/03/01 06:00 [medline]
AID - msq163 [pii]
AID - 10.1093/molbev/msq163 [doi]
PST - ppublish
SO  - Mol Biol Evol. 2010 Dec;27(12):2674-7. doi: 10.1093/molbev/msq163. Epub 2010 Jun 
      28.