PCR Analyzer v 1.02 – Estimate for Initial Amount of Amplicon Present in a PCR

PCR Analyzer v 1.02

:: DESCRIPTION

PCR Analyzer is a software to estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR.

::DEVELOPER

National Institute of Environmental Health Sciences , National Institute of Health

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PCR Analyzer

:: MORE INFORMATION

Citation

Marjo V Smith , Chris R Miller, Michael Kohn, Nigel J Walker and Chris J Portier
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process
BMC Bioinformatics 2007, 8:409doi:10.1186/1471-2105-8-409

CLONET 20140806 – CLONality Estimate in Tumors

CLONET 20140806

:: DESCRIPTION

CLONET is a collection of R scripts which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations.

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOSX
  • R

:: DOWNLOAD

 CLONET

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6.
Unraveling the clonal hierarchy of somatic genomic aberrations.
Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F.

CALIB 1.34.0 – Estimate absolute Expression levels from two color Microarray data

CALIB 1.34.0

:: DESCRIPTION

CALIB (Calibration model) is a BioConductor package for estimating absolute expression levels from two color microarray data

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CALIB

:: MORE INFORMATION

Citation

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data.
Zhao H, Engelen K, De Moor B, Marchal K.
Bioinformatics. 2007 Jul 1;23(13):1700-1. Epub 2007 May 7.

Migrate-N 3.6.8 – Estimate Population Sizes & Migration Rates

Migrate-N 3.6.8

:: DESCRIPTION

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.

It can use the following data types:

  • Sequence data using Felsenstein’s 84 model with or without site rate variation,
  • Single nucleotide polymorphism data (sequence-like data input, HAPMAP-like data input)
  • Microsatellite data using a stepwise mutation model or a brownian motion mutation model (using the repeatlength input format or the fragment-length input format),
  • Electrophoretic data using an ‘infinite’ allele model.

::DEVELOPER

Peter Beerli at Florida State University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOs / Linux / Unix

:: DOWNLOAD

Migrate-N

:: MORE INFORMATION

Genie 3.0 – Estimating Demographic History from Molecular Phylogenies

Genie 3.0

:: DESCRIPTION

Genie (Genealogy Interval Explorer) is a program for the inference of demographic history from reconstructed molecular phylogenies. It is primarily designed for the analysis of phylogenies reconstructed from highly variable viral gene sequences, but can be applied to other types of sequence data that contains a significant amount of phylogenetic information.

::DEVELOPER

Oliver Pybus & Andrew Rambaut

:: REQUIREMENTS

  • Windows /  MacOSX

:: DOWNLOAD

 Genie

:: MORE INFORMATION

Citation:

Pybus OG, Rambaut. A. 2002.
GENIE: Estimating demographic history from molecular phylogenies.
Bioinformatics 18:1404-5

CoNe 1.01 – Estimate Ne from two temporal samples

CoNe 1.01

:: DESCRIPTION

CoNe computes the likelihood of Ne given data on two temporally spaced genetic samples. The statistical model used is based on the coalescent of the gene copies drawn in the second sample, as described in Berthier et al. (Genetics 2003, 160:741-51). The Monte Carlo computations to compute the likelihood, however, were developed by Eric Anderson, and are orders of magnitude faster than previous implementations.

::DEVELOPER

Eric C. Anderson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

CoNe

:: MORE INFORMATION

Citation

Anderson, E. C.2005.
An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood.
Genetics 170(2):955-967.

Adapt-A-Rate 1.0 – Estimate the Rate of Adaptive Fixation in Population

Adapt-A-Rate 1.0

:: DESCRIPTION

Adapt-A-Rate is a program to estimate the rate of adaptive fixation in a population from sequences sampled at different points in time.

::DEVELOPER

Samir Bhatt and Oliver Pybus

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Adapt-A-Rate

:: MORE INFORMATION

Citation:

Bhatt S, Holmes EC, Pybus OG (2011)
The genomic rate of molecular adaptation of the human influenza A virus.
Molecular Biology & Evolution In press

iAdmix 0.2 – Using population allele frequencies for Computing Individual Admixture Estimates

iAdmix 0.2

:: DESCRIPTION

iAdmix is a program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping)

::DEVELOPER

Vikas Bansal, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 iAdmix

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Jan 16;16(1):4.
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations.
Bansal V, Libiger O.

mlRho 2.8 – Estimate the Population Mutation and Recombination Rates from Shotgun-Sequenced Diploid Genomes

mlRho 2.8

:: DESCRIPTION

mlRho takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, $\theta$, the sequencing error $\epsilon$, the zygosity correlation, and the population recombination rate, $\rho$

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C Compiler

:: DOWNLOAD

 mlRho

:: MORE INFORMATION

Citation

B. Haubold, P. Pfaffelhuber, and M. Lynch.
mlRho: A program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes.
Molecular Ecology, 19:277-284, 2010.

KELLER – Estimate Time-varying Interactions between Genes

KELLER

:: DESCRIPTION

KELLER is a kernel-reweighted logistic regression method for reverse engineering the dynamic interactions between genes based on their time series of expression values.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 KELLER

:: MORE INFORMATION

Citation

KELLER: estimating time-varying interactions between genes.
Song L, Kolar M, Xing EP.
Bioinformatics. 2009 Jun 15;25(12):i128-36.