Literature DB >> 17048396

A short proof that phylogenetic tree reconstruction by maximum likelihood is hard.

Sebastien Roch1.   

Abstract

Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel.

Mesh：

Year:  2006        PMID： 17048396     DOI： 10.1109/TCBB.2006.4

Source DB:  PubMed          Journal:  IEEE/ACM Trans Comput Biol Bioinform        ISSN： 1545-5963            Impact factor:   3.710


  19 in total

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Journal:  Mol Biol Evol       Date:  2009-10-15       Impact factor: 16.240

2.  Non-hereditary Maximum Parsimony trees.

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Journal:  J Math Biol       Date:  2011-08-13       Impact factor: 2.259

3.  FastTree 2--approximately maximum-likelihood trees for large alignments.

Authors:  Morgan N Price; Paramvir S Dehal; Adam P Arkin
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

4.  Identifiability and inference of non-parametric rates-across-sites models on large-scale phylogenies.

Authors:  Elchanan Mossel; Sebastien Roch
Journal:  J Math Biol       Date:  2012-08-09       Impact factor: 2.259

5.  Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning.

Authors:  Anton Suvorov; Joshua Hochuli; Daniel R Schrider
Journal:  Syst Biol       Date:  2020-03-01       Impact factor: 15.683

6.  PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination.

Authors:  Robert Lücking; Brendan P Hodkinson; Alexandros Stamatakis; Reed A Cartwright
Journal:  BMC Bioinformatics       Date:  2011-01-07       Impact factor: 3.169

7.  pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.

Authors:  Frederick A Matsen; Robin B Kodner; E Virginia Armbrust
Journal:  BMC Bioinformatics       Date:  2010-10-30       Impact factor: 3.169

8.  Polynomial supertree methods revisited.

Authors:  Malte Brinkmeyer; Thasso Griebel; Sebastian Böcker
Journal:  Adv Bioinformatics       Date:  2011-12-21

9.  MRL and SuperFine+MRL: new supertree methods.

Authors:  Nam Nguyen; Siavash Mirarab; Tandy Warnow
Journal:  Algorithms Mol Biol       Date:  2012-01-26       Impact factor: 1.405

10.  A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining.

Authors:  Mao-Zu Guo; Jian-Fu Li; Yang Liu
Journal:  BMC Bioinformatics       Date:  2008-05-28       Impact factor: 3.169
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