pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies

Bùi Quang Minh; Lê Sỹ Vinh; A. von Haeseler; Heiko A. Schmidt

doi:10.1093/bioinformatics/bti594

Abstract

IQPNNI is a program to infer maximum-likelihood phylogenetic trees from DNA or protein data with a large number of sequences. We present an improved and MPI-parallel implementation showing very good scaling and speed-up behavior.

Keywords

SpeedupPhylogenetic treeMaximum likelihoodComputer scienceScalingParallel computingStatisticsBiologyMathematicsGeneticsGene

Affiliated Institutions

Related Publications

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis

Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies ...

2006 Bioinformatics 15659 citations

IQPNNI: Moving Fast Through Tree Space and Stopping in Time

Lê Sỹ Vinh

An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast al...

2004 Molecular Biology and Evolution 169 citations

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

Heiko A. Schmidt , Korbinian Strimmer , Martin Vingron +1 more

Abstract Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13,...

2002 Bioinformatics 2549 citations

fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood

Gary J. Olsen , Hideo Matsuda , R. Hagstrom +1 more

We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on a wide variety of computers ranging from Unix w...

1994 Computer applications in the biosciences 1121 citations

Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies

Korbinian Strimmer , Arndt von Haeseler

A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method ...

1996 Molecular Biology and Evolution 2572 citations

Publication Info

Year: 2005
Type: article
Volume: 21
Issue: 19
Pages: 3794-3796
Citations: 82
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

OpenAlex

Cite This

APA Style

                            
                                
                                    Bùi Quang Minh, 
                                
                                    Lê Sỹ Vinh, 
                                
                                    A. von Haeseler
                                
                                et al.
                            
                            (2005). 
                            pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies. 
                            Computer applications in the biosciences
                            , 21
                            (19)
                            , 3794-3796.
                            https://doi.org/10.1093/bioinformatics/bti594
                        

Identifiers

DOI: 10.1093/bioinformatics/bti594