AliSim: A Fast and Versatile Phylogenetic Sequence Simulator For the Genomic Era

Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating data for training machine-learning applications. Many sequence simulation programs exist, but the most feature-rich programs tend to be rather slow, and the fastest programs tend to be feature-poor. Here, we introduce AliSim, a new tool that can efficiently simulate biologically realistic alignments under a large range of complex evolutionary models. To achieve high performance across a wide range of simulation conditions, AliSim implements an adaptive approach that combines the commonly-used rate matrix and probability matrix approach. AliSim takes 1.3 hours and 1.3 GB RAM to simulate alignments with one million sequences or sites, while popular software Seq-Gen, Dawg, and INDELible require two to five hours and 50 to 500 GB of RAM. We provide AliSim as an extension of the IQ-TREE software version 2.2, freely available at www.iqtree.org, and a comprehensive user tutorial at http://www.iqtree.org/doc/AliSim.

Dynamic earthquake sequence simulation with a SBIEM without periodic boundaries

Dynamic earthquake sequence simulation is an important tool for investigating the behavior of a fault that hosts a series of earthquakes because it solves all interrelated stages in the earthquake cycle consistently, including nucleation, propagation and arrest of dynamic rupture, afterslip, locking, and interseismic stress accumulation. Numerically simulating and resolving these phenomena, which have different time and length scales, in a single framework is challenging. A spectral boundary integral equation method (SBIEM) that makes use of a fast Fourier transform is widely used because it reduces required computational costs, even though it can only be used for a planar fault. The conventional SBIEM has a periodic boundary condition as a result of the discretization of the wavenumber domain with a regular mesh; thus, to obtain an approximate solution for a fault in an infinite medium, it has been necessary to simulate a region much longer than the source distribution. Here, I propose a new SBIEM that is free from this artificial periodic boundary condition. In the proposed method, the periodic boundaries are removed by using a previously proposed method for the simulation of dynamic rupture. The integration kernel for the elastostatic effect, which reaches infinitely far from the source, is expressed analytically and replaces the one in the conventional SBIEM. The new method requires simulation of a region only twice as long as the source distribution, so the computational costs are significantly less than those required by the conventional SBIEM to simulate a fault in an infinite medium. The effect of the distance λ between the artificial periodic boundaries was investigated by comparing solutions for a typical problem setting between the conventional and proposed SBIEM. The result showed that the artificial periodic boundaries cause overestimation of the recurrence interval that is proportional to λ−2. If λ is four times the fault length, the interval is overestimated by less than 1%. Thus, the artificial periodic boundaries have only a modest effect on the conclusions of previous studies.

Performance Evaluation of MRMED Algorithm by Monitoring BER

In this research work, we have developed a communication system (transmitter / receiver) to control peak to average power (PAPR) with small bit error rate (BER) for a 4G system called multicode code division multiple access (MCCDMA). Proposed communication system works on modified Reed Muller encoded data (MRMED) string. In MRMED data is first encoded with Reed Muller (RM) code. Thereafter, encoded RM message is XORed with optimal binary string, which results lower Peak to Average Power ratio (PAPR). A well-known fact is that, bit error rate (BER) is the best performance measurement tool for a communication system. To check the integrity of our communication system, we have run the simulation for monitoring BER using MRMED sequence. Simulation work conducted, with multipath Rayleigh fading, Minimum Shift Keying (MSK) modulation and several orders of RM codes. Our results show that implementing MRMED sequences of the suggested MCCDMA communication structure, returns noticeable lower BER. For instance, in case of RM(1,4), that has error improvement proficiency of 3 (three) errors , returns BER = 8.2x10−5 adopting MSK, at SNR = 12dB. Similarly, for RM(2,3), which has error improvement efficiency of 0 error and shows distinct BER of 4.9x10−4 at 12dB (SNR).In addition to using simulation for checking BER performance of our communication system, we have also shown in our results that, as the error improvement capability of different RM codes surges, correspondingly we get a lower BER.

An Intron of Invertebrate Microphthalmia Transcription Factor Gene Is Evolved from a Longer Ancestral Sequence

Introns are highly variable in number and size. Sequence simulation is an effective method to elucidate intron evolution patterns. Previously, we have reported that introns are more likely to evolve through mutation-and-deletion (MD) rather than through mutation-and-insertion (MI). In the present study, we further studied evolution models by allowing insertion in the MD model and by allowing deletion in the MI model at various frequencies. It was found that all deletion-biased models with proper parameter settings could generate sequences with attributes matchable to 16 invertebrate introns from the microphthalmia transcription factor gene, whereas all insertion-biased models with any parameter settings failed to generate such sequences. We conclude that the examined invertebrate introns may have evolved from a longer ancestral sequence in a deletion-biased pattern. The constructed models are useful for studying the evolution of introns from other genes and/or from other taxonomic groups. (C++ scripts of all deletion- and insertion-biased models are available upon request.)

A robust method for the identification of non-Gaussian autoregressive systems in colored Gaussian noise

This paper introduces a novel technique for parameter estimation of an autoregressive (AR) all-pole process under non-Gaussian noise environment using third order cumulants of the observed sequence. The proposed AR parameters estimation technique is based on formulating a particular structured matrix with entries of third order cumulants of the observed output sequence only. This matrix almost possesses a full rank structure. The observed sequence may be contaminated with additive Gaussian noise (white or colored), whose power spectral density is unknown. The system is driven by a zero-mean independent and identically distributed (i.i.d) non-Gaussian sequence. Simulation results confirm the good numerical conditioning of the algorithm and the improvement in performance with respect to well-known methods even when the observed signal is heavily contaminated with Gaussian noise.

A broad survey of DNA sequence data simulation tools

In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools is sparse. To address this, we performed a review of DNA sequence simulation tools developed to date and evaluated 20 state-of-art DNA sequence simulation tools on their ability to produce accurate reads based on their implemented sequence error model. We provide a succinct description of each tool and suggest which tool is most appropriate for the given different scenarios. Given the multitude of similar yet non-identical tools, researchers can use this review as a guide to inform their choice of DNA sequence simulation tool. This paves the way towards assessing existing tools in a unified framework, as well as enabling different simulation scenario analysis within the same framework.

A Time-Sequence Simulation Method for Power Unit’s Monthly Energy-Trade Scheduling with Multiple Energy Sources

The uncertainty of new energy output from wind power is rarely considered in the monthly energy-trade scheduling. This causes many problems since the new energy penetration level increases. The fairness of the scheduled energy for the power suppliers is difficult to guarantee. Because the actual power system operation is far away from scheduling when the monthly energy-trade schedule is carried out, unnecessary wind curtailment might occur, and even the feasibility of monthly energy-trade schedule might not be guaranteed. This affects the security and reliability of the power system operation. In this paper, a new time-sequence simulation method for the monthly energy-trade scheduling is proposed, which considers the new energy power forecasting characteristic and the computational load problem of hourly energy-trade simulation in the remaining months. The proposed method is based on a segment modelling strategy. The power generation in the scheduling month is optimized hourly, and the energy generation is optimized in the subsequent months on a monthly basis. For the scheduling month, accurate cost function is applied in the objective function, and detailed short-term operation constraints and the new energy forecasting results are considered, which can guarantee the feasibility of the new monthly energy-trade scheduling and lay a solid foundation for daily dispatching. For the subsequent months, since the load forecast accuracy is lower and no wind power forecasting results could be used, the rough cost function is applied, and only monthly constraints are considered. To ensure a balance in the execution progress of each power generating entity, the simulation time-scale is set as the remainder of the months in the study year. The new approach ensures the fairness of power execution progress and improves the new energy consumption level. A case study was used to verify the feasibility and effectiveness of the proposed method, which provides a theoretical reference for the monthly electrical energy-trade scheduling.