Bioinformatics Advance Access originally published online on August 23, 2006
Bioinformatics 2006 22(21):2688-2690; doi:10.1093/bioinformatics/btl446
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof. Moret, STATION 14, CH-1015 Lausanne, Switzerland
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ABSTRACT |
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 TOP ABSTRACT 1 INTRODUCTION2 OPTIMIZATIONS OF RAxML3 RESULTS AND DISCUSSION4 CONCLUSION AND FUTURE...REFERENCES |
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Summary: 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, and the use of the GTR+CAT approximation as replacement for GTR+
yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets 
4000 taxa it also runs 2–3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25 057 (1463 bp) and 2182 (51 089 bp) taxa, respectively.
Availability: icwww.epfl.ch/~stamatak
Contact: Alexandros.Stamatakis{at}epfl.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
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1 INTRODUCTION |
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TOPABSTRACT1 INTRODUCTION2 OPTIMIZATIONS OF RAxML3 RESULTS AND DISCUSSION4 CONCLUSION AND FUTURE...REFERENCES |
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Phylogenetic inference with the maximum likelihood (ML) method is NP-hard (Chor and Tuller, 2005). Despite the algorithmic complexity and the high-computational cost of ML, significant progress has been achieved with the release of fast and accurate programs such as PHYML (Guindon and Gascuel, 2003), IQPNNI (Minh et al., 2005), MrBayes (Ronquist and Huelsenbeck, 2003), GARLI (Zwickl, 2006) and RAxML (Stamatakis et al., 2005). Most of these programs allow for inference of 1000 taxon trees on a single CPU in <24 h.
This paper describes the new version of RAxML [Randomized axelerated maximum likelihood for high performance computing (RAxML-VI-HPC, v2.0.1)], which is significantly faster than the previous versions of RAxML due to simple, yet very efficient technical optimizations and a slight alteration of the search algorithm. In addition, RAxML has been parallelized with MPI to enable parallel bootstrapping and multiple inferences on distinct starting trees on PC clusters. Moreover, it implements bifurcating and multifurcating constraint trees and the capability to assign and estimate separate model parameters1 for individual genes of multi-gene alignments (mixed/partitioned models).
The main focus is on the computation of huge trees (1000 taxa) for real-world data and the comparative performance study with GARLI, IQPNNI, MrBayes and PHYML. Since the efficiency of the novel optimizations in RAxML-VI-HPC increases with the number of taxa, less significant performance improvements will be observed on smaller datasets. Performance comparisons of RAxML with other popular ML programs on smaller datasets, including simulated alignments, can be found in Hordijk and Gascuel (2005), Stamatakis et al. (2005) and Zwickl (2006). Finally, the experimental study also shows that the GTR+CAT approximation [see Stamatakis (2006) for a detailed description] can be efficiently deployed as a replacement for the significantly more compute- and memory intensive GTR+ model.
Some of the largest published ML-based analyses to date have been conducted using RAxML (Robertson et al., 2005; Ley et al., 2005, 2006). On-going work includes the computation of a backbone tree for Bacteria with 
9000 taxa, a phylogeny for Acer with 582 taxa, and the analysis of a mammalian multi-gene alignment comprising 2182 sequences.
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2 OPTIMIZATIONS OF RAxML |
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TOPABSTRACT1 INTRODUCTION2 OPTIMIZATIONS OF RAxML3 RESULTS AND DISCUSSION4 CONCLUSION AND FUTURE...REFERENCES |
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A detailed description of the optimizations listed below is provided in the on-line supplement. The main improvements cover:
- An efficient mechanism to store and re-store topologies and branch lengths via rearrangement descriptors.
- A consequent re-use of partial likelihood vectors.
- A dynamic adaptation of the rearrangement distance.
- Low-level optimization of the GTR+CAT and GTR+ likelihood functions.
- An efficient re-implementation of Maximum Parsimony starting tree computations.
An important and generally applicable insight from those optimizations is that storing and re-storing an unrooted tree topology with 2n–3 branch lengths and 2n–2 nodes can become a major performance bottleneck for trees with >1000 taxa. It is thus important to store alternative topologies as a sequence of topological changes applied to the current topology rather than as complete data object. Only the consequent avoidance of storage operations reveals the actual power of the Lazy Subtree Rearrangement (LSR) mechanism introduced in Stamatakis et al. (2005).
Another issue which becomes important for huge trees is to determine a ‘good’ rearrangement distance, i.e. re-insertion radius for the LSR moves. In RAxML-VI the algorithm initially determines the best rearrangement distance by applying distances of 5, 10, ... , 25 for one iteration of LSRs, to the starting tree. The minimum rearrangement distance which yields the best likelihood improvement on the starting tree is then selected for the inference. Despite the extra computations which are performed, a ‘good’ rearrangement distance pays off in terms of likelihood units for huge alignments with large evolutionary diameters (e.g. the 6722 and 7769 taxa alignments, see Supplementary Table 2).
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3 RESULTS AND DISCUSSION |
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TOPABSTRACT1 INTRODUCTION2 OPTIMIZATIONS OF RAxML3 RESULTS AND DISCUSSION4 CONCLUSION AND FUTURE...REFERENCES |
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The exact experimental set-up as well as the results are described in detail in the on-line supplement. Table and Figure numbers also refer to the on-line supplement.
Results in Supplementary Table 2 show that RAxML-VI-HPC clearly outperforms RAxML-V in terms of inference times. In addition, due to the usage of a ‘good’ rearrangement setting it also yields significantly better log-likelihood values on the larger and more diverse datasets 4000 taxa. Supplementary Figure 3 shows the significant computational advantages of the GTR+CAT over the GTR+ implementation in RAxML-VI.
Supplementary Tables 3–6 indicate that RAxML-VI-HPC outperforms other current sequential phylogeny programs, on huge datasets with respect to inference times, memory consumption as well as final log-likelihood values. In addition, the performance advantage with respect to run-times increases with growing alignment size (Supplementary Table 5). Another important result is that the GTR+CAT approximation (Supplementary Table 3) can be used to significantly reduce memory consumption and still yield significantly better GTR+ likelihood values (Supplementary Table 4) than competing programs.
GARLI terminated within approximately the same time as RAxML-VI-HPC on the six smaller datasets and yielded the second-best likelihood score in all cases. This is an astonishing achievement for several reasons: GARLI implements a genetic search algorithm and was executed under GTR+. Moreover, it maintains a whole population of trees in memory, including some intelligently selected (Zwickl, 2006) partial likelihood vectors as well as all tree topologies. Thus, it is expected to be slower than the RAxML hill-climbing algorithm. This extraordinary performance is due to the sophisticated implementation of the likelihood function and promising algorithmic ideas (Zwickl, 2006) such that the forthcoming publication about GARLI is surely something to look forward to. Note that, the parallel genetic search algorithm of GARLI performs a distinct and more thorough search, that yields, e.g. better final trees on the 1000 taxon alignment (Zwickl, 2006). However, the focus of the current study is on the strictly sequential versions of all programs.
The performance of the new version of MrBayes is also remarkable. Given that it has to maintain four distinct Markov chains, the relatively low memory consumption in combination with acceptable likelihood values after 60 h under GTR+, the performance is quite impressive. As Bayesian inference conceptually differs from pure ML-based inference, a comparison based on likelihood scores is certainly not fair since it uses MrBayes as an ML heuristic. MrBayes has mainly been included owing to its popularity.
IQPNNI and PHYML both suffer from a relatively inefficient technical implementation. The high memory consumption of IQPNNI and PHYML is due to a different memory organization which uses two likelihood vectors per branch (3n – 6 vectors) instead of one per inner node (n – 2 vectors).
Moreover, PHYML uses NNI moves which only exploit a very small fraction of the search space. A solution to this problem has been proposed by Hordijk and Gascuel (2005). However, the respective program is currently only available as proof-of-concept implementation (W. Hordijk and O. Gascuel, personal communication) and cannot be used for large trees owing to numerical problems.
In the final analysis, it can be stated that technical implementation aspects are becoming increasingly important and can yield significant performance improvements. In addition, in all programs there exist excellent algorithmic ideas which in the optimal case could significantly advance the field, when merged into one program.
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4 CONCLUSION AND FUTURE WORK |
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TOPABSTRACT1 INTRODUCTION2 OPTIMIZATIONS OF RAxML3 RESULTS AND DISCUSSION4 CONCLUSION AND FUTURE...REFERENCES |
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The new version VI of RAxML has been presented, which incorporates efficient technical optimizations, parallel OpenMP- and MPI-based implementations, and a mixed model implementation. A thorough experimental study on large real-world datasets shows that RAxML can find better trees with a significantly lower memory consumption within similar or less time than the best competing program.
Future work will mainly cover the development of new methods for rapid bootstrapping. Despite the fact, that RAxML and GARLI allow for inference of huge trees with ML in reasonable times, conducting a full biological analysis still requires at least 100 or 1000 bootstraps which places the computational burden much higher than for the inference of a single ML tree.
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Acknowledgments |
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The author would like to thank Derrick Zwickl, Wim Hordijk, Olivier Gascuel, B.Q. Minh, L.S. Vinh and Bret Larget for useful discussions on experimental set-up and their programs. He would also like to thank Usman Roshan, Charles Robertson, Josh Wilcox, Robin Gutell and Daniel Dalevi for providing the alignment data. Funding to pay the Open Access publication charges for this article was provided by Swiss Confederation Funding.
Conflict of Interest: none declared.
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FOOTNOTES |
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Associate Editor: Keith A Crandall
1CAT and cannot be used simultaneously in the same analysis. 
Received on May 15, 2006; revised on July 21, 2006; accepted on August 16, 2006
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REFERENCES |
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TOPABSTRACT1 INTRODUCTION2 OPTIMIZATIONS OF RAxML3 RESULTS AND DISCUSSION4 CONCLUSION AND FUTURE...REFERENCES |
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Chor, B. and Tuller, T. (2005) Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics, 21, 97–106.
Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol, . 52, 696–704
Hordijk, W. and Gascuel, O. (2005) Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics, 21, 4338–4347
Ley, R., et al. (2005) Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA, 102, 11070–11075
Ley, R.E., et al. (2006) Unexpected diversity and complexity of the guerrero negro hypersaline microbial mat. Appl. Envir. Microbiol, . 72, 3685–3695
Minh, B.Q., et al. (2005) pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics, 21, 3794–3796
Robertson, C., et al. (2005) Phylogenetic diversity and ecology of environmental Archaea. Curr. Opin. Microbiol, . 8, 638–642[Web of Science][Medline].
Ronquist, F. and Huelsenbeck, J. (2003) Mrbayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574
Stamatakis, A. (2006) Phylogenetic models of rate heterogeneity: a high performance computing perspective. Proceedings of the IPDPS2006Rhodos, Greece.
Stamatakis, A., et al. (2005) Raxml-iii: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21, 456–463
Zwickl, D. (2006) Genetic algorithm approaches for the phylogenetic analysis of large biologiical sequence datasets under the maximum likelihood criterion. PhD thesis,, TX University of Texas at Austin.
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Y. Yamanoue, M. Miya, K. Matsuura, S. Miyazawa, N. Tsukamoto, H. Doi, H. Takahashi, K. Mabuchi, M. Nishida, and H. Sakai Explosive Speciation of Takifugu: Another Use of Fugu as a Model System for Evolutionary Biology Mol. Biol. Evol., March 1, 2009; 26(3): 623 - 629. [Abstract] [Full Text] [PDF]
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M. A. Minge, J. D Silberman, R. J.S Orr, T. Cavalier-Smith, K. Shalchian-Tabrizi, F. Burki, A. Skjaeveland, and K. S Jakobsen Evolutionary position of breviate amoebae and the primary eukaryote divergence Proc R Soc B, February 22, 2009; 276(1657): 597 - 604. [Abstract] [Full Text] [PDF]
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R. C. Pratt, G. C. Gibb, M. Morgan-Richards, M. J. Phillips, M. D. Hendy, and D. Penny Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors Mol. Biol. Evol., February 1, 2009; 26(2): 313 - 326. [Abstract] [Full Text] [PDF]
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F. U. Battistuzzi and S. B. Hedges A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land Mol. Biol. Evol., February 1, 2009; 26(2): 335 - 343. [Abstract] [Full Text] [PDF]
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W. C. Lima, A. M. Varani, and C. F.M. Menck NAD Biosynthesis Evolution in Bacteria: Lateral Gene Transfer of Kynurenine Pathway in Xanthomonadales and Flavobacteriales Mol. Biol. Evol., February 1, 2009; 26(2): 399 - 406. [Abstract] [Full Text] [PDF]
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J. R. Bailey, T. P. Brennan, K. A. O'Connell, R. F. Siliciano, and J. N. Blankson Evidence of CD8+ T-Cell-Mediated Selective Pressure on Human Immunodeficiency Virus Type 1 nef in HLA-B*57+ Elite Suppressors J. Virol., January 1, 2009; 83(1): 88 - 97. [Abstract] [Full Text] [PDF]
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Y. Liu, J. W. Leigh, H. Brinkmann, M. T. Cushion, N. Rodriguez-Ezpeleta, H. Philippe, and B. F. Lang Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts Mol. Biol. Evol., January 1, 2009; 26(1): 27 - 34. [Abstract] [Full Text] [PDF]
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A. Stamatakis and M. Ott Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures Phil Trans R Soc B, December 27, 2008; 363(1512): 3977 - 3984. [Abstract] [Full Text] [PDF]
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U. S Johansson, R. C.K Bowie, S. J Hackett, and T. S Schulenberg The phylogenetic affinities of Crossley's babbler (Mystacornis crossleyi): adding a new niche to the vanga radiation of Madagascar Biol Lett, December 23, 2008; 4(6): 677 - 680. [Abstract] [Full Text] [PDF]
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C. J. Cox, P. G. Foster, R. P. Hirt, S. R. Harris, and T. M. Embley The archaebacterial origin of eukaryotes PNAS, December 23, 2008; 105(51): 20356 - 20361. [Abstract] [Full Text] [PDF]
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R. J. Gifford, A. Katzourakis, M. Tristem, O. G. Pybus, M. Winters, and R. W. Shafer From the Cover: A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution PNAS, December 23, 2008; 105(51): 20362 - 20367. [Abstract] [Full Text] [PDF]
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R. Frommolt, S. Werner, H. Paulsen, R. Goss, C. Wilhelm, S. Zauner, U. G. Maier, A. R. Grossman, D. Bhattacharya, and M. Lohr Ancient Recruitment by Chromists of Green Algal Genes Encoding Enzymes for Carotenoid Biosynthesis Mol. Biol. Evol., December 1, 2008; 25(12): 2653 - 2667. [Abstract] [Full Text] [PDF]
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M. Kutsukake, N. Nikoh, H. Shibao, C. Rispe, J.-C. Simon, and T. Fukatsu Evolution of Soldier-Specific Venomous Protease in Social Aphids Mol. Biol. Evol., December 1, 2008; 25(12): 2627 - 2641. [Abstract] [Full Text] [PDF]
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E. B. Rosenblum, J. E. Stajich, N. Maddox, and M. B. Eisen Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis PNAS, November 4, 2008; 105(44): 17034 - 17039. [Abstract] [Full Text] [PDF]
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D. E. Desjardin, A. W. Wilson, and M. Binder Durianella, a new gasteroid genus of boletes from Malaysia. Mycologia, November 1, 2008; 100(6): 956 - 961. [Abstract] [Full Text] [PDF]
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N. Poulakakis, S. Glaberman, M. Russello, L. B. Beheregaray, C. Ciofi, J. R. Powell, and A. Caccone From the Cover: Historical DNA analysis reveals living descendants of an extinct species of Galapagos tortoise PNAS, October 7, 2008; 105(40): 15464 - 15469. [Abstract] [Full Text] [PDF]
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S. A. Smith and M. J. Donoghue Rates of Molecular Evolution Are Linked to Life History in Flowering Plants Science, October 3, 2008; 322(5898): 86 - 89. [Abstract] [Full Text] [PDF]
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J. Kim and M. J. Sanderson Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap Syst Biol, October 1, 2008; 57(5): 665 - 674. [Abstract] [Full Text] [PDF]
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S. S. Renner, G. W. Grimm, G. M. Schneeweiss, T. F. Stuessy, and R. E. Ricklefs Rooting and Dating Maples (Acer) with an Uncorrelated-Rates Molecular Clock: Implications for North American/Asian Disjunctions Syst Biol, October 1, 2008; 57(5): 795 - 808. [Abstract] [Full Text] [PDF]
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E. Roberts, A. Sethi, J. Montoya, C. R. Woese, and Z. Luthey-Schulten Molecular signatures of ribosomal evolution PNAS, September 16, 2008; 105(37): 13953 - 13958. [Abstract] [Full Text] [PDF]
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A. B. Prasad, M. W. Allard, NISC Comparative Sequencing Program, and E. D. Green Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets Mol. Biol. Evol., September 1, 2008; 25(9): 1795 - 1808. [Abstract] [Full Text] [PDF]
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S. D'Aniello, M. Irimia, I. Maeso, J. Pascual-Anaya, S. Jimenez-Delgado, S. Bertrand, and J. Garcia-Fernandez Gene Expansion and Retention Leads to a Diverse Tyrosine Kinase Superfamily in Amphioxus Mol. Biol. Evol., September 1, 2008; 25(9): 1841 - 1854. [Abstract] [Full Text] [PDF]
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L. Gomez-Alpizar, C.-H. Hu, R. Oliva, G. Forbes, and J. B. Ristaino Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans Mycologia, July 1, 2008; 100(4): 590 - 602. [Abstract] [Full Text] [PDF]
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R. Burri, H. N. Hirzel, N. Salamin, A. Roulin, and L. Fumagalli Evolutionary Patterns of MHC Class II B in Owls and Their Implications for the Understanding of Avian MHC Evolution Mol. Biol. Evol., June 1, 2008; 25(6): 1180 - 1191. [Abstract] [Full Text] [PDF]
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N. Wahlberg and C. W. Wheat Genomic Outposts Serve the Phylogenomic Pioneers: Designing Novel Nuclear Markers for Genomic DNA Extractions of Lepidoptera Syst Biol, April 1, 2008; 57(2): 231 - 242. [Abstract] [Full Text] [PDF]
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A. Zuccaro, C. L. Schoch, J. W. Spatafora, J. Kohlmeyer, S. Draeger, and J. I. Mitchell Detection and Identification of Fungi Intimately Associated with the Brown Seaweed Fucus serratus Appl. Envir. Microbiol., February 15, 2008; 74(4): 931 - 941. [Abstract] [Full Text] [PDF]
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T. A. Isenbarger, M. Finney, C. Rios-Velazquez, J. Handelsman, and G. Ruvkun Miniprimer PCR, a New Lens for Viewing the Microbial World Appl. Envir. Microbiol., February 1, 2008; 74(3): 840 - 849. [Abstract] [Full Text] [PDF]
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