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Results 1 - 10
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1,949
Alignment-Free Phylogenetic Reconstruction
, 2009
"... We introduce the first polynomial-time phylogenetic reconstruction algorithm under a model of sequence evolution allowing insertions and deletions—or indels. Given appropriate assumptions, our algorithm requires sequence lengths growing polynomially in the number of leaf taxa. Our techniques are dis ..."
Abstract
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Cited by 15 (1 self)
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We introduce the first polynomial-time phylogenetic reconstruction algorithm under a model of sequence evolution allowing insertions and deletions—or indels. Given appropriate assumptions, our algorithm requires sequence lengths growing polynomially in the number of leaf taxa. Our techniques
Phylogenetic Reconstruction with Insertions and Deletions
, 2009
"... We study phylogenetic reconstruction of complete d-ary trees, with three possible mutations: substitutions, insertions and deletions. We give the first efficient algorithm for this problem which uses sequences of poly logarithmic length. The paper introduces two new tools: 1. A new distance measure, ..."
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Cited by 1 (1 self)
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We study phylogenetic reconstruction of complete d-ary trees, with three possible mutations: substitutions, insertions and deletions. We give the first efficient algorithm for this problem which uses sequences of poly logarithmic length. The paper introduces two new tools: 1. A new distance measure
Optimal phylogenetic reconstruction
- In STOC ’06: Proceedings of the thirty-eighth annual ACM symposium on Theory of computing
, 2006
"... One of the major tasks of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. This problem is of critical importance in almost all areas of biology and has a very clear mathematical formulation. The evolutionary model is given by a Markov chain on the true evolution ..."
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Cited by 43 (9 self)
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One of the major tasks of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. This problem is of critical importance in almost all areas of biology and has a very clear mathematical formulation. The evolutionary model is given by a Markov chain on the true
phylogenetic reconstruction methods*
"... This paper reports a simulation study comparing and evaluating the perfor-mance of different linguistic phylogeny reconstruction methods on model data-sets for which the true trees are known. UPGMA performed least well, then (in ascending order) neighbor joining, the method of Gray & Atkinson an ..."
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This paper reports a simulation study comparing and evaluating the perfor-mance of different linguistic phylogeny reconstruction methods on model data-sets for which the true trees are known. UPGMA performed least well, then (in ascending order) neighbor joining, the method of Gray & Atkinson
Pitfalls of heterogeneous processes for phylogenetic reconstruction
- Systematic Biology
, 2006
"... Different genes often have different phylogenetic histories. Even within regions having the same phylogenetic history, the mutation rates often vary. We investigate the prospects of phylogenetic reconstruction when all the characters are generated from the same tree topology, but the branch lengths ..."
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Cited by 15 (3 self)
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Different genes often have different phylogenetic histories. Even within regions having the same phylogenetic history, the mutation rates often vary. We investigate the prospects of phylogenetic reconstruction when all the characters are generated from the same tree topology, but the branch lengths
Genes order and phylogenetic reconstruction: Application to γ-proteobacteria
- In Proc. 3rd RECOMB Comparative Genomics Satellite Workshop, volume 3678 of LNBI
, 2005
"... Abstract. We study the problem of phylogenetic reconstruction based on gene order for whole genomes. We define three genomic distances between whole genomes represented by signed sequences, based on the matching of similar segments of genes and on the notions of breakpoints, conserved intervals and ..."
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Cited by 15 (8 self)
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Abstract. We study the problem of phylogenetic reconstruction based on gene order for whole genomes. We define three genomic distances between whole genomes represented by signed sequences, based on the matching of similar segments of genes and on the notions of breakpoints, conserved intervals
S: PhyloBayes 3. A Bayesian software package for phylogenetic reconstruction and molecular dating
- Bioinformatics
"... Motivation: A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test t ..."
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Cited by 187 (8 self)
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Motivation: A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test
A comparison of phylogenetic reconstruction methods on an IE dataset
- Transactions of the Philological Society
, 2005
"... Researchers interested in the history of the Indo-European family of languages have used a variety of methods to estimate the phylogeny of the family, and have obtained widely differing results. In this paper we explore the reconstructions of the Indo-European phylogeny obtained by using the major p ..."
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Cited by 16 (1 self)
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for these differences, and make proposals with respect to phylogenetic reconstruction in historical linguistics. 1
Empirical profile mixture models for phylogenetic reconstruction
, 2005
"... Motivation: Previous studies have shown that accounting for sitespecific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of saturation. However, such profile mix ..."
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Cited by 2 (0 self)
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Motivation: Previous studies have shown that accounting for sitespecific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of saturation. However, such profile
Results 1 - 10
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1,949
