LinuxLinks.com
Newbies What Next ? News Forums Calendar

Search





News Sections
Home
General News (3987/0)
Reviews (637/0)
Press Releases (465/0)
Distributions (197/0)
Software (911/0)
Hardware (537/0)
Security (192/0)
Tutorials (356/0)
Off Topic (181/0)


User Functions
Username:

Password:

Don't have an account yet? Sign up as a New User


Events
There are no upcoming events




simuPOP

simuPOP

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.

Easy simulations like most models in standard population genetics books can be setup easily, whereas very complicated simulations such as spreading of complex diseases, ancient out-of-africa migrations can be built step by step by adding appropriate operators (objects that work on populations).

The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios.

 simuPOP 1.1.6

Price
Free to download

Size
9.5MB
License

GNU GPL v3

Developer
Bo Peng

Website
simupop.sourceforge.net

System Requirements
Python

Optional
R
rpy
wxPython

Support:
Documentation, User's Guide, Reference Manual, Mailing List, SourceForge Project Page

Selected Reviews:

Features include:

  • Provides three types of modules that use 1, 8 or >=32 bits to store an allele
  • Supports autosome, chromosome X, chromosome Y, and mitochondrial chromosomes as a special case of a group of customized chromosome types
  • An arbitrary number of float numbers, called information fields, can be attached to individuals of a population
  • No limit on number of homologous sets of chromosomes, the size of the genome, or the number of individuals in a population
  • Provides more than 70 operators that cover all important aspects of genetic studies:
    • Mutation (k-allele, stepwise, generalized stepwise and hybrid)
    • Migration (arbitrary, can create new subpopulation)
    • Recombination and gene conversion (uniform or nonuniform, sex-specific)
    • Quantitative trait (single, multilocus or hybrid)
    • Selection (single-locus, additive, multiplicative or hybrid multi-locus models)
    • Penetrance (single, multi-locus or hybrid)
    • Ascertainment (case–control, affected sibpairs, random, nuclear and large pedigree)
    • Statistics calculation (including but not limited to allele, genotype, haplotype, heterozygote number and frequency; expected heterozygosity; di-allelic and multi-allelic , and linkage disequilibrium measures)
    • Pedigree tracing
    • Visualization (using R or other Python modules)
    • Load/save in simuPOP’s native format and many external formats such as Linkage
  • Scripting interface
  • Comprehensive documentation

simuPOP in action

Return to Biology Tools Home Page

Bookmark and Share


Last Updated Monday, May 25 2015 @ 12:29 PM EDT


We have written a range of guides highlighting excellent free books for popular programming languages. Check out the following guides: C, C++, C#, Java, JavaScript, CoffeeScript, HTML, Python, Ruby, Perl, Haskell, PHP, Lisp, R, Prolog, Scala, Scheme, Forth, SQL, Node.js (new), Fortran (new), Erlang (new), Pascal (new), and Ada (new).


Group Tests
100 Essential Apps
All Group Tests


Top Free Software
5 Office Suites
3 Lean Desktops
7 Document Processors
4 Distraction Free Tools
9 Project Management
4 Business Solutions
9 Groupware Apps
14 File Managers
10 Databases
21 Backup Tools
21 Productivity Tools
5 Note Taking Apps
9 Terminal Emulators
21 Financial Tools
5 Bitcoin Clients
21 Text Editors
21 Video Emulators
21 Home Emulators
42 Graphics Apps
6 CAD Apps
42 Scientific Apps
10 Web Browsers
42 Email Apps
12 Instant Messaging
10 IRC Clients
7 Twitter Clients
12 News Aggregators
11 VoIP Apps
42 Best Games
9 Steam Games
42 Audio Apps
5 Music Streaming
42 Video Apps
5 YouTube Tools
80 Security Apps
9 System Monitoring
8 Geometry Apps
Free Console Apps
14 Multimedia
4 Audio Grabbers
9 Internet Apps
3 HTTP Clients
5 File Managers
Programming
8 Compilers
9 IDEs
9 Debuggers
7 Revision Control Apps
6 Doc Generators
Free Web Software
21 Web CMS
14 Wiki Engines
8 Blog Apps
6 eCommerce Apps
5 Human Resource Apps
10 ERP
10 CRM
6 Data Warehouse Apps
8 Business Intelligence
6 Point-of-Sale

Other Articles
Migrating from Windows
Back up your data
20 Free Linux Books
24 Beginner Books
12 Shell Scripting Books


Older Stories
Sunday 04/12
  • First Peek at XBian on the Raspberry Pi 2 (0)

  • Saturday 04/04
  • First Look at OSMC RC on the Raspberry Pi 2 (0)

  • Sunday 03/29
  • First Steps with OpenELEC on the Raspberry Pi 2 (0)
  • Ubuntu MATE 15.04 for Raspberry Pi 2 (0)

  • Monday 03/16
  • MIPS Creator CI20 v Raspberry Pi 2 (0)
  • Raspberry Pi 2: Raspbian (ARMv6) v Linaro (ARMv7) (0)

  • Friday 03/06
  • Raspberry Pi 2 review (0)

  • Sunday 02/22
  • Chess in a Few Bytes (0)
  • Learn the Art of Computer Programming With These Great Free Beginner Books (2)
  • CD Audio Grabbers (0)


  • Vote

    What Linux distribution do you run on your main computer?

    Debian
    Fedora
    Mint
    Slackware
    openSuSE
    Arch
    Ubuntu
    Redhat
    Mageia
    CentOS
    FreeBSD
    Results
    829 votes | 3 comments

    Built with GeekLog and phpBB
    Comments to the webmaster are welcome
    Copyright 2009 LinuxLinks.com - All rights reserved