pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies

被引：51

作者：

Minh, BQ

Vinh, LS

von Haeseler, A ^{[1
]}

Schmidt, HA

机构：

[1] Univ Dusseldorf, D-4000 Dusseldorf, Germany

[2] NIC, FZ Julich, Julich, Germany

[3] Univ Freiburg, Freiburg, Germany

来源：

BIOINFORMATICS | 2005年 / 21卷 / 19期

关键词：

D O I：

10.1093/bioinformatics/bti594

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 speedup behavior.

引用

页码：3794 / 3796

页数：3

共 17 条

[1] Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference [J].

Altekar, G ;

Dwarkadas, S ;

Huelsenbeck, JP ;

Ronquist, F .

BIOINFORMATICS, 2004, 20 (03) :407-415

[2]

Brent R. P., 1973, ALGORITHMS MINIMIZAT

[3]

Chor B, 2005, LECT NOTES COMPUT SC, V3500, P296

[4] EVOLUTIONARY TREES FROM DNA-SEQUENCES - A MAXIMUM-LIKELIHOOD APPROACH [J].

FELSENSTEIN, J .

JOURNAL OF MOLECULAR EVOLUTION, 1981, 17 (06) :368-376

[5] BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data [J].

Gascuel, O .

MOLECULAR BIOLOGY AND EVOLUTION, 1997, 14 (07) :685-695

[6] A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood [J].

Guindon, S ;

Gascuel, O .

SYSTEMATIC BIOLOGY, 2003, 52 (05) :696-704

[7] DATING OF THE HUMAN APE SPLITTING BY A MOLECULAR CLOCK OF MITOCHONDRIAL-DNA [J].

HASEGAWA, M ;

KISHINO, H ;

YANO, TA .

JOURNAL OF MOLECULAR EVOLUTION, 1985, 22 (02) :160-174

[8] DPRml: distributed phylogeny reconstruction by maximum likelihood [J].

Keane, TM ;

Naughton, TJ ;

Travers, SAA ;

McInerney, JO ;

McCormack, GP .

BIOINFORMATICS, 2005, 21 (07) :969-974

[9]

OLSEN GJ, 1994, COMPUT APPL BIOSCI, V10, P41

[10] TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing [J].

Schmidt, HA ;

Strimmer, K ;

Vingron, M ;

von Haeseler, A .

BIOINFORMATICS, 2002, 18 (03) :502-504

← 1 2 →