RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies

Bioinformatics

Volumn 30, Issue 9, 2014, Pages 1312-1313

  Stamatakis, Alexandros ^a,b  

^a HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^b KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; HIGH THROUGHPUT SEQUENCING; PHYLOGENY; STATISTICAL MODEL;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SOFTWARE;

EID: 84899553363     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu033     Document Type: Article

References (16)

1. Aberer, A.J. et al. (2010) Parallelized phylogenetic post-analysis on multi-core architectures. J. Comput. Sci., 1, 107-114.
2. Berger, S.A. and Stamatakis, A. (2010) Accuracy of morphology-based phylogenetic fossil placement under maximum likelihood. In: International Conference on Computer Systems and Applications (AICCSA), 2010 IEEE/ACS. IEEE, New York, USA, pp. 1-9.
3. Berger, S.A. et al. (2011) Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol., 60, 291-302.
4. Dao, D. et al. (2013) Automated plausibility analysis of large phyolgenies. Technical report. Karlsruhe Institute of Technology.
5. Guindon, S. et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of phyml 3.0. Syst. Biol., 59, 307-321.
6. Izquierdo-Carrasco, F. et al. (2011) Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinformatics, 12, 470.
7. Le, S.Q. et al. (2012) Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol. Biol. Evol., 29, 2921-2936.
8. Lewis, P.O. (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol., 50, 913-925.
9. Minh, B.Q. et al. (2013) Ultrafast approximation for phylogenetic bootstrap. Mol. Biol Evol., 30, 1188-1195.
10. Pattengale, N.D. et al. (2010) How many bootstrap replicates are necessary? J. Comput. Biol., 17, 337-354.
11. Pattengale, N.D. et al. (2011) Uncovering hidden phylogenetic consensus in large data sets. IEEE/ACM Trans. Comput. Biol. Bioinforma., 8, 902-911.
12. Pfeiffer, W. and Stamatakis, A. (2010) Hybrid mpi/pthreads parallelization of the raxml phylogenetics code. In International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW), 2010 IEEE. IEEE, New York, USA, pp. 1-8.
13. Salichos, L. and Rokas, A. (2013) Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 497, 327-331.
14. Stamatakis, A. (2006) Raxml-vi-hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
15. Stamatakis, A. and Aberer, A. (2013) Novel parallelization schemes for large-scale likelihood-based phylogenetic inference. In IEEE 27th International Symposium on Parallel Distributed Processing (IPDPS), 2013. pp. 1195-1204.
16. Stamatakis, A. et al. (2008) A rapid bootstrap algorithm for the raxml web servers. Syst. Biol., 57, 758-771.