Literature DB >> 16046495

pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies.

Bui Quang Minh1, Le Sy Vinh, Arndt von Haeseler, Heiko A Schmidt.   

Abstract

SUMMARY: 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.

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Mesh：

Year:  2005        PMID： 16046495     DOI： 10.1093/bioinformatics/bti594

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  23 in total

1.  Nodal signalling determines biradial asymmetry in Hydra.

Authors:  Hiroshi Watanabe; Heiko A Schmidt; Anne Kuhn; Stefanie K Höger; Yigit Kocagöz; Nico Laumann-Lipp; Suat Ozbek; Thomas W Holstein
Journal:  Nature       Date:  2014-08-24       Impact factor: 49.962

2.  Many-core algorithms for statistical phylogenetics.

Authors:  Marc A Suchard; Andrew Rambaut
Journal:  Bioinformatics       Date:  2009-04-15       Impact factor: 6.937

3.  Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures.

Authors:  Alexandros Stamatakis; Michael Ott
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2008-12-27       Impact factor: 6.237

4.  Unifying vertical and nonvertical evolution: a stochastic ARG-based framework.

Authors:  Erik W Bloomquist; Marc A Suchard
Journal:  Syst Biol       Date:  2009-11-09       Impact factor: 15.683

5.  PCA and clustering reveal alternate mtDNA phylogeny of N and M clades.

Authors:  G Alexe; R Vijaya Satya; M Seiler; D Platt; T Bhanot; S Hui; M Tanaka; A J Levine; G Bhanot
Journal:  J Mol Evol       Date:  2008-10-15       Impact factor: 2.395

6.  PALM: a paralleled and integrated framework for phylogenetic inference with automatic likelihood model selectors.

Authors:  Shu-Hwa Chen; Sheng-Yao Su; Chen-Zen Lo; Kuei-Hsien Chen; Teng-Jay Huang; Bo-Han Kuo; Chung-Yen Lin
Journal:  PLoS One       Date:  2009-12-07       Impact factor: 3.240

7.  FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods.

Authors:  Stephanie Zierke; Jason D Bakos
Journal:  BMC Bioinformatics       Date:  2010-04-12       Impact factor: 3.169

8.  Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling.

Authors:  Alexandros Stamatakis; Markus Göker; Guido W Grimm
Journal:  Evol Bioinform Online       Date:  2010-05-24       Impact factor: 1.625

9.  A TolC-like protein is required for heterocyst development in Anabaena sp. strain PCC 7120.

Authors:  Suncana Moslavac; Kerstin Nicolaisen; Oliver Mirus; Fadi Al Dehni; Rafael Pernil; Enrique Flores; Iris Maldener; Enrico Schleiff
Journal:  J Bacteriol       Date:  2007-08-24       Impact factor: 3.490

10.  TonB-dependent transporters and their occurrence in cyanobacteria.

Authors:  Oliver Mirus; Sascha Strauss; Kerstin Nicolaisen; Arndt von Haeseler; Enrico Schleiff
Journal:  BMC Biol       Date:  2009-10-12       Impact factor: 7.431
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