MaCS 0.5d

:: DESCRIPTION

MaCS is a simulator of the coalescent process that simulates geneologies spatially across chromosomes as a Markovian process. The algorithm is similar to the SMC algorithm (McVean and Cardin, Phil Trans Soc R B 2005) in that the algorithm scales linearly in time with respect to sample size and sequence length. However, it more accurately models the true coalescent, while supporting all demographic scenarios found in the popular program MS (Hudson, Bioinformatics 2002) making this program appropriate for simulating data for structured populations in genome wide association studies.

::DEVELOPER

Gary K. Chen, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler
Boost libraries

:: DOWNLOAD

MaCS

:: MORE INFORMATION

Citation

Genome Res. 2009 Jan;19(1):136-42. Epub 2008 Nov 24.
Fast and flexible simulation of DNA sequence data.
Chen GK, Marjoram P, Wall JD.

MACS 2.2.5

:: DESCRIPTION

MACS (Model-based Analysis for ChIP-Seq) empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples

::DEVELOPER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Tag: MACS

MaCS 0.5d – Markovian Coalescent Simulator

MaCS 0.5d

MACS 2.2.5 – Analyze Data Generated by Short Read Sequencer

MACS 2.2.5