Tag: Estimation

ProteinEvolverABC – Estimation of Recombination and Substitution Rates in Alignments of Protein Sequences

ProteinEvolverABC

:: DESCRIPTION

The package ProteinEvolverABC is a computer framework to estimate recombination and substitution rates in multiple alignments of protein sequences by approximate Bayesian computation.

::DEVELOPER

CME Group

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

ProteinEvolverABC

:: MORE INFORMATION

Citation

Arenas M.
ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation.
Bioinformatics. 2021 Aug 27:btab617. doi: 10.1093/bioinformatics/btab617. Epub ahead of print. PMID: 34450622.

get_size_NN v1 – Neutral Network Size Estimation

get_size_NN v1

:: DESCRIPTION

get_size_NN calculates, via nested Monte Carlo, an estimate of the size of the neutral set (network) of a given RNA secondary structure.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 get_size_NN

:: MORE INFORMATION

Citation:

Thomas Jörg, Olivier C Martin and Andreas Wagner
Neutral network sizes of biological RNA molecules can be computed and are atypically large.
BMC Bioinformatics 2008, 9:464

RNANumbers – Estimation of RNA numbers of Spots Intensities

RNANumbers

:: DESCRIPTION

  • RNANumbers (Estimation of fluorescence-tagged RNA numbers from spot intensities)

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlabs

:: DOWNLOAD

RNANumbers

:: MORE INFORMATION

Citation:

Häkkinen A, Kandhavelu M, Garasto S, Ribeiro AS.
Estimation of fluorescence-tagged RNA numbers from spot intensities.
Bioinformatics. 2014 Apr 15;30(8):1146-1153. doi: 10.1093/bioinformatics/btt766. Epub 2014 Jan 2. PMID: 24389660.

 

BEST 1.0.1 – Binding-site Estimation Suite of Tools

BEST 1.0.1

:: DESCRIPTION

BEST is a suite of motif-finding programs, including four motif-finding programs: AlignACE, BioProspector, Consensus, MEME, and the optimization program BioOptimizer configured for each of these program

::DEVELOPER

Jun Liu

:: SCREENSHOTS

 BEST

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BEST

:: MORE INFORMATION

Citation

Che D., Jensen, S., Cai, L. and Liu JS.
BEST: Binding-site Estimation Suite of Tools.
Bioinformatics, 21(12):2909-2911.

SIBIS 1.0 – Bayesian model for Inconsistent Protein Sequence Estimation

SIBIS 1.0

:: DESCRIPTION

SIBIS (Bayesian Inconsistency in Sequences) is designed to detect such inconsistencies based on the evolutionary information in multiple sequence alignments. A Bayesian framework, combined with Dirichlet mixture models, is used to estimate the probability of observing specific amino acids and to detect inconsistent or erroneous sequence segments.

::DEVELOPER

Julie Dawn Thompson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SIBIS

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 13. pii: btu329. [Epub ahead of print]
SIBIS: A Bayesian model for inconsistent protein sequence estimation.
Khenoussi W1, Vanhoutrève R1, Poch O1, Thompson JD2.

LEADMIX 1.0 – Likelihood Estimation of ADMIXture

LEADMIX 1.0

:: DESCRIPTION

LEADMIX is a Fortran program to estimate the admixture proportions and genetic drift using data on genetic markers

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Fortran 90/95 compiler

:: DOWNLOAD

 LEADMIX

:: MORE INFORMATION

Citation

Wang, J. (2003)
Maximum Likelihood Estimation of Admixture Proportions from Genetic Data.
Genetics 164: 747-765.

MIMAR 20101217 – MCMC Estimation of the Isolation-Migration model Allowing for Recombination

MIMAR 20101217

:: DESCRIPTION

MIMAR (MCMC estimation of the Isolation-Migration model Allowing for Recombination) is a Markov chain Monte Carlo method to estimate parameters of an isolation-migration model. It uses summaries of polymorphism data at multiple loci surveyed in a pair of diverging populations or closely related species and in contrast to previous methods, allows for intralocus recombination. Note that you need to know the ancestral allele at each polymorphic site in order to calculate the summary statistics.

::DEVELOPER

Przeworski lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MIMAR

:: MORE INFORMATION

Citation:

Becquet and Przewroski (2007)
A new approach to estimate parameters of speciation models with application to apes
Genome Res. 2007. 17: 000

PhysioFit 1.0.2 – Estimation of Extracellular Fluxes and Growth Rate

PhysioFit 1.0.2

:: DESCRIPTION

PhysioFit is a scientific tool designed to i) quantify exchange (production and consumption) fluxes and ii) cell growth rate during (batch) cultivations of microorganisms. Fluxes are estimated from time-course measurements of extracellular metabolites and biomass concentrations.

::DEVELOPER

MetaSys

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsx
  • R

:: DOWNLOAD

PhysioFit

:: MORE INFORMATION

GVCBLUP 3.9 / GVCeasy 1.3 – Genomic Prediction and Variance Component Estimation

GVCBLUP 3.9 / GVCeasy 1.3

:: DESCRIPTION

GVCBLUP is a computer package for genomic prediction and variance component estimation for additive and dominance effects using SNP markers.

GVCeasy is the graphical user interface for the GVCBLUP package.

::DEVELOPER

The authors of GVCBLUP:
Chunkao Wang, Dzianis Prakapenka, Shengwen Wang,
H. Birali Runesha and Yang Da

The authors of GVCeasy:
Sujata Pulugurta, Chunkao Wang, Dzianis Prakapenka,
H. Birali Runesha, Yang Da

, Department of Animal Science, University of Minnesota

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

GVCBLUP  , GVCeasy

:: MORE INFORMATION

Citation

Da Y, Wang C, Wang S, Hu G (2014)
Mixed Model Methods for Genomic Prediction and Variance Component Estimation of Additive and Dominance Effects Using SNP Markers.
PLoS ONE 9(1): e87666. doi:10.1371/journal.pone.0087666.

RidgeRace – Ridge Regression for Continuous Ancestral Character Estimation on Phylogenetic Trees

RidgeRace

:: DESCRIPTION

RidgeRace is a tool to reconstruct ancestral character states and phenotypic rates.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RidgeRace

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Sep 1;30(17):i527-i533. doi: 10.1093/bioinformatics/btu477.
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees.
Kratsch C, McHardy AC.

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