TY - JOUR
T1 - Approximate maximum parsimony and ancestral maximum likelihood
AU - Alon, Noga
AU - Chor, Benny
AU - Pardi, Fabio
AU - Rapoport, Anat
N1 - Funding Information:
Many thanks to Alexander Zelikovsky for his help in clarifying some subtle points in existing Steiner approximation algorithms. The work of Noga Alon was supported in part by the Israel Science Foundation, by a USA-Israel BSF grant, and by the Hermann Minkowski Minerva Center for Geometry at Tel Aviv University. Part of this work was done while Benny Chor was visiting the European Bioinformatics Institute, Hinxton, Cambridge, UK.
PY - 2010/1
Y1 - 2010/1
N2 - We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.
AB - We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.
KW - Ancestral maximum likelihood
KW - Approximation algorithms.
KW - Biology and genetics
KW - Combinatorial algorithms
KW - Computations on discrete structures
KW - Constrained optimization
KW - Maximum parsimony
KW - Phylogenetic reconstruction
KW - Steiner trees
KW - Trees
UR - http://www.scopus.com/inward/record.url?scp=76849097970&partnerID=8YFLogxK
U2 - 10.1109/TCBB.2008.13
DO - 10.1109/TCBB.2008.13
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C2 - 20150680
AN - SCOPUS:76849097970
VL - 7
SP - 183
EP - 187
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics
SN - 1545-5963
IS - 1
M1 - 4429176
ER -