PSPE – Simulate Evolution of Non-coding DNA Sequences

PSPE

:: DESCRIPTION

PSPE (Phylogenetic Simulation of Promoter Evolution) is a computational tool specifically designed for simulating evolution of non-coding DNA sequences, in particular promoter sequences.

::DEVELOPER

PSPE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PSPE

:: MORE INFORMATION

Citation

Weichun Huang, Joseph R Nevins, and Uwe Ohler,
Phylogenetic simulation of promoter evolution: estimation and modelling of binding site turnover events and assessing their impact on alignment tools,
Genome Biology, Vol 8 (10) 2007

Microsat – Simulates the Evolution of Linked and unlinked Microsatellites using the Coalescent

Microsat

:: DESCRIPTION

Microsat reads coalescent genealogies generated by Richard Hudson’s ms, and translates them into short tandem repeat (STR, or microsatellite) datasets using the single step mutation model (SMM).

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 Microsat

:: MORE INFORMATION

bnpsd 1.2.3 – Model and Simulate Admixed Populations

bnpsd 1.2.3

:: DESCRIPTION

bnpsd (Balding-Nichols Pritchard-Stephens-Donnelly) is an R package to model and simulate admixed populations

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

bnpsd

:: MORE INFORMATION

Citation

Ochoa, Alejandro, and John D. Storey. 2016a.
FST And Kinship for Arbitrary Population Structures I: Generalized Definitions.”
bioRxiv doi:10.1101/083915.

Ochoa, Alejandro, and John D. Storey. 2016b.
FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators.
bioRxiv doi:10.1101/083923.

Pyvolve v1.0.1 – Python Library to Simulate Evolutionary Sequence data

Pyvolve v1.0.1

:: DESCRIPTION

Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution.

::DEVELOPER

Claus Wilke’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pyvolve

:: MORE INFORMATION

Citation

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies.
Spielman SJ, Wilke CO.
PLoS One. 2015 Sep 23;10(9):e0139047. doi: 10.1371/journal.pone.0139047.

simNGS 20130502 – Simulate Observations from Illumina NGS machines

simNGS 20130502

:: DESCRIPTION

simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data (“dust”, bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 simNGS

:: MORE INFORMATION

SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Seq-Gen

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Jun;13(3):235-8.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A1, Grassly NC.

simMSG – Simulate Accuracy of MSG for your Genome

simMSG

:: DESCRIPTION

SimMSG allows users to simulate hybrids from crossing two parental genomes, and run the MSG (Multiplexed Shotgun Genotyping) pipeline on these simulated hybrids to test the accuracy of the algorithm. It allows researchers to decide on various parameters before they conduct an MSG experiment.

::DEVELOPER

Ray Cui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SimMSG

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2015 May 28. doi: 10.1111/1755-0998.12434.
simMSG: an experimental design tool for high-throughput genotyping of hybrids.
Schumer M, Cui R, Rosenthal GG, Andolfatto P,

invertFREGENE – Simulate Sequence Level data with Inversions

invertFREGENE

:: DESCRIPTION

invertFREGENE is a software for simulating sequence level data with inversions

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 invertFREGENE

:: MORE INFORMATION

Citation

Paul F. O’Reilly, Lachlan J. M. Coin and Clive J. Hoggart
invertFREGENE: software for simulating inversions in population genetic data
Bioinformatics (2010) 26 (6): 838-840.

polyester 1.6.0 – Simulate RNA-seq Reads

polyester 1.6.0

:: DESCRIPTION

Polyester is an R package designed to simulate RNA-seq data, beginning with an experimental design and ending with collections of RNA-seq reads

::DEVELOPER

Alyssa Frazee <alyssa.frazee at gmail.com>, Jeff Leek <jtleek at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 Polyester

:: MORE INFORMATION

Citation:

Polyester: simulating RNA-seq datasets with differential transcript expression.
Frazee AC, Jaffe AE, Langmead B, Leek JT.
Bioinformatics. 2015 Apr 28. pii: btv272.