Filters








4,652 Hits in 3.4 sec

Enumerating phylogenetic trees with multiple labels

L.R. Foulds, R.W. Robinson
1988 Discrete Mathematics  
Here we determine exact and asymptotic numbers for two classes of trees in which multiple vertex labels are allowed.  ...  Evolutionary trees are used in biology to illustrate postulated ancestral relationships between species and are often called phylogenetic trees.  ...  The method used to derive cases 1 and 2 from the previously analyzed singleton-label cases is a general one, which could have been applied to the other multiple-label classes of phylogenetic trees analysed  ... 
doi:10.1016/0012-365x(88)90201-4 fatcat:g7c7fgy44rgs5oglx6dvt6vkqy

Enumerating Phylogenetic Trees with Multiple Labels [chapter]

L.R. Foulds, R.W. Robinson
1988 Annals of Discrete Mathematics  
Here we determine exact and asymptotic numbers for two classes of trees in which multiple vertex labels are allowed.  ...  Evolutionary trees are used in biology to illustrate postulated ancestral relationships between species and are often called phylogenetic trees.  ...  The method used to derive cases 1 and 2 from the previously analyzed singleton-label cases is a general one, which could have been applied to the other multiple-label classes of phylogenetic trees analysed  ... 
doi:10.1016/s0167-5060(08)70778-7 fatcat:skbels7k4bgk5i2zkyf2msqbwq

NON-RECURSIVE ENUMERATION OF HETEROCHRONOUS TREES

P.F. Slade
2018 International Journal of Pure and Applied Mathematics  
These enumeration formulae measure sample spaces of Bayesian prior distributions of trees relevant to theoretical and computational phylogenetics.  ...  The enumeration formula of a non-contemporaneous genealogy with total sample size n = n1 + n2 requires a nested sum-product.  ...  Acknowledgments Research commenced while a Postdoctoral Scientist with the Computational Biology and Bioinformatics Unit at the Australian National University.  ... 
doi:10.12732/ijpam.v117i1.17 fatcat:so4n7oryijarjbuqzh37rcsgoe

Tanglegrams: a reduction tool for mathematical phylogenetics [article]

Frederick A Matsen IV, Sara Billey, Arnold Kas, Matjaž Konvalinka
2015 arXiv   pre-print
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees.  ...  Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.  ...  Thus, labeled tanglegrams are in one-to-one correspondence with pairs of leaf-labeled phylogenetic trees.  ... 
arXiv:1507.04784v1 fatcat:k34oz3bwsfh2vadqyr2l66fmb4

The Worst Case Complexity of Maximum Parsimony

Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson
2014 Journal of Computational Biology  
One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related  ...  The input to this problem is a multiple alignment of n input sequences of length m each, and a topology in the form of a rooted phylogenetic tree over n leaves, where each leaf is associated with a distinct  ...  It follows that the number of children of v with label k is the number of trees T in F v with label(T ) > k.  ... 
doi:10.1089/cmb.2014.0128 pmid:25302568 pmcid:PMC4224053 fatcat:mwqfyewfbre2hlp3y6aut6zy3i

The Worst Case Complexity of Maximum Parsimony [chapter]

Amir Carmel, Noa Musa-Lempel, Dekel Tsur, Michal Ziv-Ukelson
2014 Lecture Notes in Computer Science  
One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related  ...  The input to this problem is a multiple alignment of n input sequences of length m each, and a topology in the form of a rooted phylogenetic tree over n leaves, where each leaf is associated with a distinct  ...  It follows that the number of children of v with label k is the number of trees T in F v with label(T ) > k.  ... 
doi:10.1007/978-3-319-07566-2_9 fatcat:uz4uqk5dxza5ppmju5bdyw3wnm

Tanglegrams: A Reduction Tool for Mathematical Phylogenetics

Frederick A. Matsen, Sara C. Billey, Arnold Kas, Matjaz Konvalinka
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees.  ...  Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.  ...  Thus, labeled tanglegrams are in one-to-one correspondence with pairs of leaflabeled phylogenetic trees.  ... 
doi:10.1109/tcbb.2016.2613040 pmid:28113515 fatcat:tn2zm25n7rhdnd3otdrnnkvlgm

Most Compact Parsimonious Trees [article]

Dimitris Papamichail, Angela Huang, Andrew Miller, Edward Kennedy, Jan-Lucas Ott, Georgios Papamichail
2016 arXiv   pre-print
In this article we prove some unique properties of most parsimonious live phylogenetic trees with polytomies, and describe novel algorithms to find the such trees without resorting to exhaustive enumeration  ...  Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed.  ...  Phylogenetic trees can be rooted or unrooted, and their edges are labelled with lengths that correspond to evolutionary distances between species.  ... 
arXiv:1603.03315v2 fatcat:5qvxovvayvajxd3mbnn5ecct4q

Page 793 of Mathematical Reviews Vol. , Issue 90B [page]

1990 Mathematical Reviews  
W. (1-GA-S) Enumerating phylogenetic trees with multiple labels. Proceedings of the First Japan Conference on Graph Theory and Applications (Hakone, 1986). Discrete Math. 72 (1988), no. 1-3, 129-139.  ...  Saul Stahl (1-KS) 90b:05067 05C30 05C05 90B10 Liu, Bo Lian (PRC-SCN) Enumeration of oriented trees and free trees with a given number of leaves.  ... 

Discovering Frequent Agreement Subtrees from Phylogenetic Data

S. Zhang, j.T.L. Wang
2008 IEEE Transactions on Knowledge and Data Engineering  
Furthermore, each leaf in the tree has a label representing a taxon (species or organism) name, whereas internal nodes are unlabeled.  ...  We first develop a novel canonical form for rooted trees together with a phylogeny-aware tree expansion scheme for generating candidate subtrees level by level.  ...  Vincent Berry for his responding to our request for the source code of his MAST program and exchanging interesting ideas on the FAST problem with us.  ... 
doi:10.1109/tkde.2007.190676 fatcat:oxi2k6bxt5g43kchbaai6l6dwq

EvoMiner: frequent subtree mining in phylogenetic databases

Akshay Deepak, David Fernández-Baca, Srikanta Tirthapura, Michael J. Sanderson, Michelle M. McMahon
2013 Knowledge and Information Systems  
Here we present EvoMiner, a new algorithm for mining frequent subtrees in collections of phylogenetic trees.  ...  Our algorithm achieves speed-ups of up to 100 times or more over Phylominer, the current state-of-the-art algorithm for mining phylogenetic trees.  ...  Pattengale for sharing the datasets consisting of bootstrapped trees. A special thanks to the anonymous reviewers at KAIS whose detailed comments helped greatly in improving the paper.  ... 
doi:10.1007/s10115-013-0676-0 fatcat:xhm5phofffekxkeas34f6otkd4

Approximation algorithms for constrained generalized tree alignment problem

Srikrishnan Divakaran
2009 Discrete Applied Mathematics  
In many instances of this problem partial phylogenetic tree for S is known.  ...  phylogenetic trees that specify the topological constraints that an evolutionary tree of S needs to satisfy, construct a minimum cost evolutionary tree for S.  ...  We typically refer to a fully labeled tree as an evolutionary tree and a tree with only the leaves labeled as phylogenetic tree.  ... 
doi:10.1016/j.dam.2008.10.009 fatcat:z2d4i5hmyvdcxgzxmw2nlvwi2e

A fast tool for minimum hybridization networks

Zhi-Zhong Chen, Lusheng Wang, Satoshi Yamanaka
2012 BMC Bioinformatics  
In this case, we want to combine the two phylogenetic trees into a hybridization network with the fewest hybridization events.  ...  Despite this disadvantage, our experimental data shows that FastHN runs substantially faster than the multi-threaded Dendroscope 3 on a PC with multiple cores.  ...  Basically, HNE is the problem of enumerating a representative set of minimum hybridization networks of two given phylogenetic trees.  ... 
doi:10.1186/1471-2105-13-155 pmid:22748099 pmcid:PMC3434172 fatcat:gixifdxqcffzpn5g4tdcjdin5u

A new phylogenetic tree model for fuzzy characters

A. Auyeung
2005 International Conference on Information Technology: Coding and Computing (ITCC'05) - Volume II  
This dissertation proposes a new phylogenetic tree model, called fuzzy phylogeny. Fuzzy phylogeny is an extension of a classic phylogenetic model, called perfect phylogeny.  ...  A phylogenetic tree for perfect phylogeny is called a PP-tree and a PP-tree T for the matrix M is a rooted tree that satisfies: 1. each object labels exactly one node in T; 2. each edge is labeled by at  ...  The perfect phylogeny problem is to verify whether a given set of species with a set of characters forms a phylogenetic tree and, if it does, to construct the corresponding phylogenetic tree.  ... 
doi:10.1109/itcc.2005.22 dblp:conf/itcc/Auyeung05 fatcat:px3ipjoye5cflpzp5uh6oppdie

Brauer and partition diagram models for phylogenetic trees and forests [article]

Andrew Francis, Peter D Jarvis
2022 arXiv   pre-print
We furthermore extend the Diaconis-Holmes correspondence from binary trees to non-binary trees and to forests, showing for instance that the set of all forests is in bijection with the set of partitions  ...  We introduce a correspondence between phylogenetic trees and Brauer diagrams, inspired by links between binary trees and matchings described by Diaconis and Holmes (1998).  ...  When the authors began exploring the potential for modeling phylogenetic trees with Brauer diagrams, they made the fortunate decision to ask James East for advice.  ... 
arXiv:2111.15225v3 fatcat:qytk26pz5ze6pno2zp4tq6kjp4
« Previous Showing results 1 — 15 out of 4,652 results