Alignment-Free phylogenetic reconstruction

Authors:
Constantinos Daskalakis;Sebastien Roch
Affiliations:
CSAIL, MIT;Department of Mathematics and Bioinformatics Progam, UCLA
Venue:
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Year:
2010

Citing 12
Cited 1

A few logs suffice to build (almost) all trees: part II

Theoretical Computer Science
A few logs suffice to build (almost) all trees (l): part I

Random Structures & Algorithms
Provably Fast and Accurate Recovery of Evolutionary Trees through Harmonic Greedy Triplets

SIAM Journal on Computing
Inverting Random Functions II: Explicit Bounds for Discrete Maximum Likelihood Estimation, with Applications

SIAM Journal on Discrete Mathematics
On the complexity of distance-based evolutionary tree reconstruction

SODA '03 Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms
Optimal phylogenetic reconstruction

Proceedings of the thirty-eighth annual ACM symposium on Theory of computing
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

Bioinformatics
Distorted Metrics on Trees and Phylogenetic Forests

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast and reliable reconstruction of phylogenetic trees with very short edges

Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
Sequence Length Requirement of Distance-Based Phylogeny Reconstruction: Breaking the Polynomial Barrier

FOCS '08 Proceedings of the 2008 49th Annual IEEE Symposium on Foundations of Computer Science
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep

RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Maximal accurate forests from distance matrices

RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology

Recovering the tree-like trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis

RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology

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Abstract

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 distance-based and largely bypass the problem of multiple alignment.