PMID- 11719567
OWN - NLM
STAT- MEDLINE
DCOM- 20020212
LR  - 20180109
IS  - 0737-4038 (Print)
IS  - 0737-4038 (Linking)
VI  - 18
IP  - 12
DP  - 2001 Dec
TI  - Reliabilities of parsimony-based and likelihood-based methods for detecting 
      positive selection at single amino acid sites.
PG  - 2179-85
AB  - The reliabilities of parsimony-based and likelihood-based methods for inferring 
      positive selection at single amino acid sites were studied using the nucleotide 
      sequences of human leukocyte antigen (HLA) genes, in which positive selection is 
      known to be operating at the antigen recognition site. The results indicate that 
      the inference by parsimony-based methods is robust to the use of different 
      evolutionary models and generally more reliable than that by likelihood-based 
      methods. In contrast, the results obtained by likelihood-based methods depend on 
      the models and on the initial parameter values used. It is sometimes difficult to 
      obtain the maximum likelihood estimates of parameters for a given model, and the 
      results obtained may be false negatives or false positives depending on the 
      initial parameter values. It is therefore preferable to use parsimony-based 
      methods as long as the number of sequences is relatively large and the branch 
      lengths of the phylogenetic tree are relatively small.
FAU - Suzuki, Y
AU  - Suzuki Y
AD  - Institute of Molecular Evolutionary Genetics, Department of Biology, The 
      Pennsylvania State University, University Park 16802, USA. yis1@psu.edu
FAU - Nei, M
AU  - Nei M
LA  - eng
GR  - GM20293/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, P.H.S.
PL  - United States
TA  - Mol Biol Evol
JT  - Molecular biology and evolution
JID - 8501455
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Amino Acid Substitution
MH  - *Evolution, Molecular
MH  - HLA Antigens/chemistry/*genetics
MH  - Humans
MH  - *Likelihood Functions
MH  - Models, Genetic
MH  - *Selection, Genetic
EDAT- 2001/11/24 10:00
MHDA- 2002/02/13 10:01
CRDT- 2001/11/24 10:00
PHST- 2001/11/24 10:00 [pubmed]
PHST- 2002/02/13 10:01 [medline]
PHST- 2001/11/24 10:00 [entrez]
AID - 10.1093/oxfordjournals.molbev.a003764 [doi]
PST - ppublish
SO  - Mol Biol Evol. 2001 Dec;18(12):2179-85. doi: 
      10.1093/oxfordjournals.molbev.a003764.