scholarly journals discoal: flexible coalescent simulations with selection

2016 ◽  
Author(s):  
Andrew D. Kern ◽  
Daniel R. Schrider
Keyword(s):  
Programming Language ◽  
Source Code ◽  
Recurrent Mutation ◽  
Supplementary Information ◽  
Selective Sweeps ◽  
C Programming Language ◽  
Coalescent Simulations ◽  
C Programming ◽  
Soft Selective Sweeps ◽  
General Public License

AbstractSummaryHere we describe discoal, a coalescent simulator able to generate population samples that include selective sweeps in a feature-rich, flexible manner. discoal can perform simulations conditioning on the fixation of an allele due to drift or either hard or soft selective sweeps—even those occurring a large genetic distance away from the simulated locus. discoal can simulate sweeps with recurrent mutation to the adaptive allele, recombination, and gene conversion, under nonequilibrium demographic histories and without specifying an allele frequency trajectory in advance.Availability and ImplementationAvailability and implementation: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kernlab/discoal_multipop) under a GNU General Public [email protected] informationSupplementary Figures and Text are appended below

scholarly journals Implementation of Lexical Analysis on Assignment Statements in C++ Programming Language

2020 ◽  
pp. 269-273
Author(s):  
Zaw Lin Oo ◽  
Mya Sandar Kyin
Keyword(s):  
Programming Language ◽  
Semantic Analysis ◽  
Source Code ◽  
Target Language ◽  
Lexical Analysis ◽  
Syntax Analysis ◽  
C Programming Language ◽  
Front End ◽  
C Programming ◽  
Assignment Statement

A compiler is a computer program that translates computer code written in one programming language (the source language) into another language (the target language). The name compiler is primarily used for programs that translate source code from a high-level programming language to a lower level language [7]. The three main processes of compilation are lexical analysis, syntax analysis and semantic analysis. A compiler has two components, front-end and back-end. Front-end portion of a compiler has to do to main tasks lexical analysis and syntax analysis. On the lexical analysis, input source code are scanned and tokenized into various tokens [6]. In the system, front-end portion of the compiler, lexical analysis is used. There are many token elements in C++ programming language. In this system, line break token, white space tokens (space and tab) and operators (+,-,*,/,=,+= and so on) are used as token elements for the assignment statements of C++ source program. This system is taken all the assignment statements of C++ program as input. Of course, the extracted assignment statements may be literals or values assignment statement (e.g. x=3; or pi= 3.142;), variable assignment statement (e.g. x=y; or x=z;) and expression assignment statement (e.g. a=b+c; or x=y*z; or a=b*(c+d); and produced symbol table, step by step recognized table by using finite state automata and lexeme table.

scholarly journals SFS_CODE: More Efficient and Flexible Forward Simulations

2015 ◽  
Author(s):  
Ryan D. Hernandez ◽  
Lawrence H. Uricchio
Keyword(s):  
Human Genome ◽  
Open Source Software ◽  
General Public ◽  
Population Genetic ◽  
Genome Structure ◽  
Supplementary Information ◽  
Selective Sweeps ◽  
Complex Models ◽  
Soft Selective Sweeps ◽  
General Public License

SUMMARY: Modern implementations of forward population genetic simulations are efficient and flexible, enabling the exploration of complex models that may otherwise be intractable. Here we describe an updated version of SFS_CODE, which has increased efficiency and includes many novel features. Among these features is an arbitrary model of dominance, the ability to simulate partial and soft selective sweeps, as well as track the trajectories of mutations and/or ancestries across multiple populations under complex models that are not possible under a coalescent framework. We also release sfs_coder, a Python wrapper to SFS_CODE allowing the user to easily generate command lines for common models of demography, selection, and human genome structure, as well as parse and simulate phenotypes from SFS_CODE output. Availability and Implementation: Our open source software is written in C and Python, and are available under the GNU General Public License at http://sfscode.sourceforge.net. Contact: [email protected] Supplementary information: Detailed usage information is available from the project website at http://sfscode.sourceforge.net.

scholarly journals Parallel programming technologies on computer complexes

2020 ◽  
Vol 30 (3) ◽  
pp. 28-33 ◽  
Author(s):  
S. A. Pryadko ◽  
A. Yu. Troshin ◽  
V. D. Kozlov ◽  
A. E. Ivanov
Keyword(s):  
Parallel Programming ◽  
Shared Memory ◽  
Programming Language ◽  
Operating Systems ◽  
Distributed Memory ◽  
Programming Models ◽  
Writing Programs ◽  
Advantages And Disadvantages ◽  
C Programming Language ◽  
C Programming

The article describes various options for speeding up calculations on computer systems. These features are closely related to the architecture of these complexes. The objective of this paper is to provide necessary information when selecting the capability for the speeding process of solving the computation problem. The main features implemented using the following models are described: programming in systems with shared memory, programming in systems with distributed memory, and programming on graphics accelerators (video cards). The basic concept, principles, advantages, and disadvantages of each of the considered programming models are described. All standards for writing programs described in the article can be used both on Linux and Windows operating systems. The required libraries are available and compatible with the C/C++ programming language. The article concludes with recommendations on the use of a particular technology, depending on the type of task to be solved.

scholarly journals Computing support for testing equal values of the figurative numbers in the Pascal triangle

2020 ◽  
Vol 2 (7) ◽  
pp. 36-41
Author(s):  
Miroslava Mihajlov Carević ◽  
Miloš Ilić ◽  
Milena Petrović ◽  
Nebojša Denić
Keyword(s):  
Programming Language ◽  
Mathematical Analysis ◽  
Computer Laboratory ◽  
C Programming Language ◽  
Pascal Triangle ◽  
C Programming ◽  
Computing Support

In this paper we deal with a method for the determination of numbers in a Pascal triangle that are simultaneously triangular, tetrahedral and pentaedroidni. The collected results, obtained by mathematical analysis, were verified by computer. For this purpose, we used the C# programming language as well as the computer laboratory within our University in order to test the results. The results collected by computer confirmed the accuracy of the results obtained by mathematical analysis.

Sign in / Sign up

Export Citation Format

Share Document