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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A. Stamatakis A. Bioinformatics. 2014 May 1;30(9):1312-3. doi: 10.1093/bioinformatics/btu033. Epub 2014 Jan 21. Bioinformatics. 2014. PMID: 24451623 Free PMC article.
RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. ...RESULTS: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substi …
RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likel …
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
Stamatakis A, Ludwig T, Meier H. Stamatakis A, et al. Bioinformatics. 2005 Feb 15;21(4):456-63. doi: 10.1093/bioinformatics/bti191. Epub 2004 Dec 17. Bioinformatics. 2005. PMID: 15608047
It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods such as parsimony or neighbor joining. Due to the combinatorial and computational co …
It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to th …
AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method.
Stamatakis AP, Ludwig T, Meier H, Wolf MJ. Stamatakis AP, et al. Proc IEEE Comput Soc Bioinform Conf. 2002;1:21-8. Proc IEEE Comput Soc Bioinform Conf. 2002. PMID: 15838120
This paper introduces AxML, a program derived from fastDNAml, incorporating a fast topology evaluation function. The algorithmic optimizations introduced, represent a general approach for accelerating this function and are applicable to both sequential and pa …
This paper introduces AxML, a program derived from fastDNAml, incorporating a fast topology evaluation function. The algorithm …
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Stamatakis A. Stamatakis A. Bioinformatics. 2006 Nov 1;22(21):2688-90. doi: 10.1093/bioinformatics/btl446. Epub 2006 Aug 23. Bioinformatics. 2006. PMID: 16928733
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, an …
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for infer …
AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa.
Stamatakis A, Auch AF, Meier-Kolthoff J, Göker M. Stamatakis A, et al. BMC Bioinformatics. 2007 Oct 22;8:405. doi: 10.1186/1471-2105-8-405. BMC Bioinformatics. 2007. PMID: 17953748 Free PMC article.
The parallel analysis with AxParafit on 128 CPUs for a medium-sized dataset with an 512 by 512 association matrix is more than 1,200/128 times faster per processor than the sequential Parafit run. ...We outline the substantial benefits of using parallel AxParafit by exampl …
The parallel analysis with AxParafit on 128 CPUs for a medium-sized dataset with an 512 by 512 association matrix is more than 1,200/ …
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures.
Stamatakis A, Ott M. Stamatakis A, et al. Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3977-84. doi: 10.1098/rstb.2008.0163. Philos Trans R Soc Lond B Biol Sci. 2008. PMID: 18852107 Free PMC article.
Initially, we present a method and an appropriate data structure to efficiently compute the likelihood score on 'gappy' multi-gene alignments. ...A first proof-of-concept implementation in RAXML indicates that this approach can accelerate inferences on large and gap …
Initially, we present a method and an appropriate data structure to efficiently compute the likelihood score on 'gappy' multi-gene al …
A rapid bootstrap algorithm for the RAxML Web servers.
Stamatakis A, Hoover P, Rougemont J. Stamatakis A, et al. Syst Biol. 2008 Oct;57(5):758-71. doi: 10.1080/10635150802429642. Syst Biol. 2008. PMID: 18853362
Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets-either with respect to the number of taxa or base pairs-can easily require a month of run time. ...These Web servers offer the possibility to conduct …
Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets-either with respe …
Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data.
Stamatakis A, Alachiotis N. Stamatakis A, et al. Bioinformatics. 2010 Jun 15;26(12):i132-9. doi: 10.1093/bioinformatics/btq205. Bioinformatics. 2010. PMID: 20529898 Free PMC article.
A property that characterizes phylogenomic datasets is that they tend to be gappy, i.e. can contain taxa with (many and disparate) missing genes. ...RESULTS: On a large phylogenomic DNA dataset with 2177 taxa, 68 genes and a gappyness of 90%, we achieve a
A property that characterizes phylogenomic datasets is that they tend to be gappy, i.e. can contain taxa with (many and disparate) mi
PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination.
Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA. Lücking R, et al. BMC Bioinformatics. 2011 Jan 7;12:10. doi: 10.1186/1471-2105-12-10. BMC Bioinformatics. 2011. PMID: 21214904 Free PMC article.
In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. ...A GTR, MK, or ORDERED model can be applied to analyse the PICS-Ord codes partition, with GTR performing slightly better than MK and ORDERE …
In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. ...A
Result verification, code verification and computation of support values in phylogenetics.
Stamatakis A, Izquierdo-Carrasco F. Stamatakis A, et al. Brief Bioinform. 2011 May;12(3):270-9. doi: 10.1093/bib/bbq079. Epub 2011 Jan 21. Brief Bioinform. 2011. PMID: 21257650
Program verification represents a largely underestimated problem in computational science that can have fatal effects on scientific conclusions....
Program verification represents a largely underestimated problem in computational science that can have fatal effects on scientific c …
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