jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.

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jModelTest: Phylogenetic Model Averaging

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.

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ModelFinder: fast model selection for accurate phylogenetic estimates

Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. 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. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources. (Maximum likelihood; phylogenetic inference; rapid bootstrap; RAxML; support values.)

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A Rapid Bootstrap Algorithm for the RAxML Web Servers

In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.

/pdf/partitionfinder-combined-selection-of-partitioning-schemes-2gsjpr8ec8.pdf

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

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In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner. We start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. We demonstrate that in simple simulations, statistical methods of model selection are indeed robust and likely to be useful for protein model selection. We have investigated patterns of amino acid substitution among homologous sequences from the three Domains of life and our results show that no single amino acid matrix is optimal for any of the datasets. Perhaps most interestingly, we demonstrate that for two large datasets derived from the proteobacteria and archaea, one of the most favored models in both datasets is a model that was originally derived from retroviral Pol proteins. This demonstrates that choosing protein models based on their source or method of construction may not be appropriate.

/pdf/assessment-of-methods-for-amino-acid-matrix-selection-and-3wg86a4905.pdf

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Several attacks are proposed against the double random phase encryption scheme. These attacks are demonstrated on computer-generated ciphered images. The scheme is shown to be resistant against brute force attacks but susceptible to chosen and known plaintext attacks. In particular, we describe a technique to recover the exact keys with only two known plain images. We compare this technique to other attacks proposed in the literature.

Resistance of the double random phase encryption against various attacks

We present the results of applying lossless and lossy data compression to a three-dimensional object reconstruction and recognition technique based on phase-shift digital holography. We find that the best lossless (Lempel-Ziv, Lempel-Ziv-Welch, Huffman, Burrows-Wheeler) compression rates can be expected when the digital hologram is stored in an intermediate coding of separate data streams for real and imaginary components. The lossy techniques are based on subsampling, quantization, and discrete Fourier transformation. For various degrees of speckle reduction, we quantify the number of Fourier coefficients that can be removed from the hologram domain, and the lowest level of quantization achievable, without incurring significant loss in correlation performance or significant error in the reconstructed object domain.

/pdf/compression-of-digital-holograms-for-three-dimensional-3l4b2nrlig.pdf

Compression of digital holograms for three-dimensional object reconstruction and recognition

A three-dimensional (3D) object reconstruction technique that uses only phase information of a phase-shifting digital hologram and a phase-only spatial-light modulator is proposed. It is well known that a digital hologram can store both amplitude and phase information of an optical electric field and can reconstruct the original 3D object in a computer. We demonstrate that it is possible to reconstruct optically 3D objects using only phase information of the optical field calculated from phase-shifting digital holograms. The use of phase-only information enables us to reduce the amount of data in the digital hologram and reconstruct optically the 3D objects using a liquid-crystal spatial light modulator without optical power loss. Numerical evaluation of the reconstructed 3D object is presented.

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Real-time three-dimensional object reconstruction by use of a phase-encoded digital hologram.

The Fourier plane encryption algorithm is subjected to a known-plaintext attack. The simulated annealing heuristic algorithm is used to estimate the key, using a known plaintext-ciphertext pair, which decrypts the ciphertext with arbitrarily low error. The strength of the algorithm is tested by using this estimated key to decrypt a different ciphertext which was also encrypted using the same original key. We assume that the plaintext is amplitude-encoded real-valued image, and analyze only the mathematical algorithm rather than a real optical system that can be more secure. The Fourier plane encryption algorithm is found to be susceptible to a known-plaintext heuristic attack.

/pdf/a-known-plaintext-heuristic-attack-on-the-fourier-plane-f2itmawh8z.pdf

Thomas J. Naughton

Papers

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Resistance of the double random phase encryption against various attacks

Compression of digital holograms for three-dimensional object reconstruction and recognition

Real-time three-dimensional object reconstruction by use of a phase-encoded digital hologram.

A known-plaintext heuristic attack on the Fourier plane encryption algorithm.