Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees

Roshan, Usman; Warnow, Tandy; Moret, Bernard M. E.; Williams, Tiffani L.

doi:10.1109/csb.2004.1332422

Cited by 73 publications

(125 citation statements)

References 23 publications

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“…The CIPRES Portal V 1.0 permitted users to run the community tree inference tools GARLI [9], RAxML [10], PAUP [11], and MrBayes [12], both as standalone tools, and with the tool Rec-I-DCM3, a disc covering method to speed and improve inference of large trees [13]. The demand for Tree Inference analyses on the CIPRES Portal quickly exceeded the computational resources available to the project, pointing to a need to redesign the CIPRES Portal for greater scalability while minimizing costs for the sake of sustainability.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Harrington

Jackes

Barrett

et al. 2012

Aust. Systematic Bot.

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Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPUhour at unit priority).

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Section: Introductionmentioning

confidence: 99%

Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Harrington

Jackes

Barrett

et al. 2012

Aust. Systematic Bot.

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“…a fraction of the species), infer optimal trees for these subsets, then finally combine these trees into a larger tree. The first implementations of this strategy have been based on quartets including four species 175 and DISK-COVERING METHODS using larger species subsets are currently being developed 176 . The combination of the supermatrix and supertree approaches (BOX 2) might thus represent a solution for reconstructing -32 -phylogenomic trees with thousands of species in order to eventually obtain a full picture of the tree of life 40,177 .…”

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confidence: 99%

Phylogenomics and the reconstruction of the tree of life

2005

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Correspondence to H.P. email: herve.philippe@umontreal.ca -2 - PrefaceAs more complete genomes are sequenced, phylogenetic analysis is entering a new era -that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms based on the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to a number of fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life may prove difficult, if not impossible, to resolve with confidence. Introductory paragraphUnderstanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. The notion of phylogeny follows directly from the theory of evolution presented by Charles Darwin in "The Origin of Species" 1 : the only illustration in his famous book is the first representation of evolutionary relationships among species, in the form of a phylogenetic tree. The subsequent enthusiasm of biologists for the phylogenetic concept is illustrated by the publication of Ernst Haeckel's famous "trees" as early as 1866 2 .Today, phylogenetics -the reconstruction of evolutionary history -relies on using mathematical methods to infer the past from features of contemporary species, with only the fossil record to provide a window on the evolutionary past of life on our planet. This reconstruction involves the identification of HOMOLOGOUS CHARACTERS that are shared among different organisms, and the inference of phylogenetic trees from the comparison of these characters using reconstruction methods (BOX 1). The accuracy of -3 -the inference is therefore heavily dependent upon the quality of models for the evolution of such characters. Because the underlying mechanisms are not yet well understood, reconstructing the evolutionary history of life on Earth based solely on the information provided by living organisms has turned out to be difficult.Until the 1970s, which brought the dawn of molecular techniques for sequencing proteins and DNA, phylogenetic reconstruction was essentially based on the analysis of morphological or ultrastructural characters. The comparative anatomy of fossils and extant species has proved powerful in some respects; for example, the main groups of animals and plants have been delineated fairly easily using these methods. However, this approach is hampered by the limited number of reliable homologous characters available; these are almost non-existent in micro-organisms 3 and are rare even in complex organisms.The introduction of the use of molecular data in phylogenetics 4 led to a revolution.In the late 1980s, access to DNA sequences increased the number of homologous characters that could be compared from less than 100 to more than 1,000, ...

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“…The above experimental results show that our strategies on the B&B phylogeny reconstruction are efficient. [Huson et al, 1999a, Huson et al, 1999b, Nakhleh et al, 2001, Roshan et al, 2004b] are a family of divide-and-conquer methods designed to "boost" the performance of existing phylogenetic reconstruction methods. All DCMs proceed in four major phases: (i) decomposing the dataset, (ii) solving the subproblems, (iii) merging the subproblems, and (iv) refining the resulting tree.…”

Section: Resultsmentioning

confidence: 99%

High‐Performance Phylogeny Reconstruction Under Maximum Parsimony

Williams¹,

Bader

Yan

et al. 2005

Parallel Computing for Bioinformatics and Computational Biology

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The similarity of the molecular matter of the organisms on Earth suggest that they all share a common ancestor. Thus any set of species is related, and this relationship is called a phylogeny. The links (or evolutionary relationships) among a set of organisms (or taxa) form a phylogenetic tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. Scientists are interested in evolutionary trees for the usual reasons of scientific curiosity. However, phylogenetic analysis is not just an academic exercise. Phylogenies are the organizing principle for most biological knowledge. As such, they are a crucial tool in identifying emerging diseases, predicting disease outbreaks, and protecting ecosystems from invasive species [Bader et al., 2001, Cracraft, 2002. The greatest impact of phylogenetics will be reconstructing the Tree of Life, the evolutionary history of all-known organisms. No one precisely knows the number of organisms that exist in the world.Estimates often cited range from 10 -100 million species. Today, only about 1.7

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Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees

Abstract: Phylogenetic trees are commonly reconstructed based on hard optimization problems such as maximum parsimony (MP) and maximum likelihood (ML

Cited by 73 publications

References 23 publications

Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Phylogenomics and the reconstruction of the tree of life

High‐Performance Phylogeny Reconstruction Under Maximum Parsimony

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