LAMARC 2.1.10 – Maximum Likelihood & Bayesian Estimation of Population Parameters

LAMARC 2.1.10

:: DESCRIPTION

LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data.

::DEVELOPER

Felsenstein/Kuhner lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX

:: DOWNLOAD

LAMARC

:: MORE INFORMATION

Citation:

Mary K. Kuhner
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Bioinformatics (2006) 22 (6): 768-770.

SiGN-SSM 1.3.0 / SiGN-L1 1.1.0 – Gene Network Estimation Software

SiGN-SSM 1.3.0 / SiGN-L1 1.1.0

:: DESCRIPTION

SiGN-SSM is open source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by the statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.

SiGN-L1 is network estimation software using sparse learning. It uses L1-regularization for simultaneous parameter estimation and model selection of statistical graphical models such as graphical Gaussian models and vector autoregressive models.

::DEVELOPER

SiGN-SSM TEam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

SiGN-SSM , SiGN-L1

:: MORE INFORMATION

Citation

Tamada, Y., Yamaguchi, R., Imoto, S., Hirose, O., Yoshida, R., Nagasaki, M., and Miyano, S. (2011).
SiGN-SSM: open source parallel software for estimating gene networks with state space models.
Bioinformatics. 2011 Apr 15;27(8):1172-3. doi: 10.1093/bioinformatics/btr078.

Genome Inform. 2011;25(1):40-52.
Sign: large-scale gene network estimation environment for high performance computing.
Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S.

EM-SNP – Allele Frequency Estimation, SNP Detection and Association Studies

EM-SNP

:: DESCRIPTION

EM-SNP is an unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
R

:: DOWNLOAD

EM-SNP

:: MORE INFORMATION

Citation

Quan Chen and Fengzhu Sun (2013):
A unified approach for allele frequency estimation, SNP detection and association studies on pooled sequencing data using EM algorithms.
BMC Genomics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2164-14-S1-S1.

micropower – Power Estimation for Microbiome Studies

micropower

:: DESCRIPTION

The micropower package is designed to facilitate power estimation for microbiome studies that will be analyzed with pairwise distances (beta diversity) and PERMANOVA (a non-parametric extension of multivariate analysis of variance to a matrix of pairwise distances).

::DEVELOPER

Bushman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

micropower

:: MORE INFORMATION

Citation

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA.
Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H.
Bioinformatics. 2015 Mar 29. pii: btv183.

Phyto-PhyloPars – Phylogenetic approach to the Estimation of Phytoplankton Traits

Phyto-PhyloPars

:: DESCRIPTION

Phyto-PhyloPars web server takes an evolutionary perspective to the variability across phytoplankton taxa in order to estimate the size, maximum growth rate, phosphate affinity and susceptibility to predation of any phytoplankton taxon, based on over one thousand observations on freshwater species.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bruggeman, J. (2011)
A phylogenetic approach to the estimation of phytoplankton traits.
Journal of Phycology 47(1): 52-65.

PhyloPars – Estimation of Missing Parameter Values using Phylogeny

PhyloPars

:: DESCRIPTION

PhyloPars provides an efficient and statistically consistent method of combining any number of empirical observations with the phylogenetic tree to arrive at complete set of estimates for missing parameter values.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W179-84. doi: 10.1093/nar/gkp370.
PhyloPars: estimation of missing parameter values using phylogeny.
Bruggeman J1, Heringa J, Brandt BW.

ReMixT v0.5.18 – Clone-specific Genomic Structure Estimation in Cancer

ReMixT v0.5.18

:: DESCRIPTION

ReMixT is a tool for joint inference of clone specific segment and breakpoint copy number in whole genome sequencing data. The input for the tool is a set of segments, a set of breakpoints predicted from the sequencing data, and normal and tumour bam files. Where multiple tumour samples are available, they can be analyzed jointly for additional benefit.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Python

:: DOWNLOAD

ReMixT

:: MORE INFORMATION

Citation

ReMixT: clone-specific genomic structure estimation in cancer.
McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-C?té A, Aparicio S, Sahinalp SC, Shah SP.
Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2.

Data2Dynamics 170117 – Modeling Environment Tailored to Parameter Estimation in Dynamical System

Data2Dynamics 170117

:: DESCRIPTION

The Data2Dynamics software package is a collection of numerical methods for quantitative dynamic modeling and a comprehensive model and data description language. The software facilitates the construction of dynamical models for biochemical reaction networks, but is not limited to this.

::DEVELOPER

D2D development team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
MatLab

:: DOWNLOAD

Data2Dynamics

:: MORE INFORMATION

Citation:

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.
Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, Vanlier J, T?nsing C, Adlung L, Engesser R, Mader W, Heinemann T, Hasenauer J, Schilling M, H?fer T, Klipp E, Theis F, Klingmüller U, Sch?berl B, Timmer J.
Bioinformatics. 2015 Jul 3. pii: btv405.

BAli-Phy 3.6.0 – Bayesian Alignment and Phylogeny estimation

BAli-Phy 3.6.0

:: DESCRIPTION

BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

::DEVELOPER

BAli-Phy team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX / Windows

:: DOWNLOAD

BAli-Phy

:: MORE INFORMATION

Citation

Suchard MA and Redelings BD
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny,
Bioinformatics, 22:2047-2048, 2006.

CEM 0.9.1 – Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads

CEM 0.9.1

:: DESCRIPTION

CEM is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

CEM

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2914-21. doi: 10.1093/bioinformatics/bts559. Epub 2012 Oct 11.
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
Li W1, Jiang T.