TY - GEN
T1 - A faster construction of greedy consensus trees
AU - Gawrychowski, Paweł
AU - Landau, Gad M.
AU - Sung, Wing Kin
AU - Weimann, Oren
N1 - Publisher Copyright: © Paweł Gawrychowski, Gad M. Landau, Wing-Kin Sung, and Oren Weimann;.
PY - 2018/7/1
Y1 - 2018/7/1
N2 - A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It is also central for predicting a species tree from a set of gene trees, as indicated recently in [Nature 2013]. This paper focuses on two of the most well-known and widely used consensus tree methods: the greedy consensus tree and the frequency di erence consensus tree. Given k conflicting trees each with n leaves, the previous fastest algorithms for these problems were O(kn2) for the greedy consensus tree [J. ACM 2016] and O(min(kn2, k2n)) for the frequency di erence consensus tree [ACM TCBB 2016]. We improve these running times to O(kn1.5) and O(kn) respectively.
AB - A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It is also central for predicting a species tree from a set of gene trees, as indicated recently in [Nature 2013]. This paper focuses on two of the most well-known and widely used consensus tree methods: the greedy consensus tree and the frequency di erence consensus tree. Given k conflicting trees each with n leaves, the previous fastest algorithms for these problems were O(kn2) for the greedy consensus tree [J. ACM 2016] and O(min(kn2, k2n)) for the frequency di erence consensus tree [ACM TCBB 2016]. We improve these running times to O(kn1.5) and O(kn) respectively.
KW - Dynamic trees
KW - Greedy consensus trees
KW - Phylogenetic trees
UR - https://www.scopus.com/pages/publications/85049774980
U2 - 10.4230/LIPIcs.ICALP.2018.63
DO - 10.4230/LIPIcs.ICALP.2018.63
M3 - Conference contribution
T3 - Leibniz International Proceedings in Informatics, LIPIcs
BT - 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018
A2 - Kaklamanis, Christos
A2 - Marx, Daniel
A2 - Chatzigiannakis, Ioannis
A2 - Sannella, Donald
PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
T2 - 45th International Colloquium on Automata, Languages, and Programming, ICALP 2018
Y2 - 9 July 2018 through 13 July 2018
ER -