Tag: Estimation

CoNCoS 0.2 – Copy Number Estimation with Controlled Support

CoNCoS 0.2

:: DESCRIPTION

CoNCoS is a tool for researchers concerned with copy number estimation from next-generation sequencing data.It detects copy number aberrations and outputs a list composed of their position, copy number and affected gene(s).

::DEVELOPER

CoNCoS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • JRE

:: DOWNLOAD

 CoNCoS

:: MORE INFORMATION

Citation

CoNCoS: Copy number estimation in cancer with controlled support.
Abdallah AT, Fischer M, Nürnberg P, Nothnagel M, Frommolt P.
J Bioinform Comput Biol. 2015 Sep 4:1550027.

Psafe 20120530 – Pooled Sequencing Allele Frequency Estimation

Psafe 20120530

:: DESCRIPTION

Psafe is a pipeline to adjust the biases and errors of sequencing data to gain more accurate allele frequency estimation.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • Perl

:: DOWNLOAD

 Psafe

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 Sep;36(6):549-60. doi: 10.1002/gepi.21648. Epub 2012 Jun 6.
Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples.
Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H.

LDhelmet 1.10 – Fine-scale Recombination Rate Estimation

LDhelmet 1.10

:: DESCRIPTION

LDhelmet is a software program for statistical inference of fine-scale crossover recombination rates from population genetic data.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 LDhelmet

:: MORE INFORMATION

Citation

Chan, A.H., Jenkins, P.A., and Song, Y.S.
Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.
PLoS Genetics, vol. 8 no. 12 (2012) e1003090.

influx_s 5.4.0 – Estimation of Metabolic Fluxes and Metabolite Concentrations

influx_s 5.4.0

:: DESCRIPTION

influx_s is a scientific software for estimation of metabolic fluxes and metabolite concentrations in a stationary framework.

::DEVELOPER

MetaSys

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsx
  • R
  • Python

:: DOWNLOAD

 influx_s

:: MORE INFORMATION

Citation

influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labeling experiments
Serguei Sokol, Pierre Millard and Jean-Charles Portais
Bioinformatics 2012 Mar 1;28(5):687-93

stochprofML 2.0.3 – Stochastic Profiling using Maximum Likelihood Estimation

stochprofML 2.0.3

:: DESCRIPTION

stochprofML is an R package of parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

::DEVELOPER

Biostatistics, Institute of Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
:: DOWNLOAD

 stochprofML

:: MORE INFORMATION

Citation:

Amrhein L, Fuchs C.
stochprofML: stochastic profiling using maximum likelihood estimation in R.
BMC Bioinformatics. 2021 Mar 15;22(1):123. doi: 10.1186/s12859-021-03970-7. PMID: 33722188; PMCID: PMC7958472.

mhsmm 0.4.16 – Parameter Estimation and Prediction for Hidden Markov and semi-Markov models for data with multiple Observation Sequences

mhsmm 0.4.16

:: DESCRIPTION

mhsmm is a software of parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. The software is suitable for equidistant time series data, with multivariate and/or missing data.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

  mhsmm

:: MORE INFORMATION

Citation

Jared O’Connell, Soren Hojsgaard (2011).
Hidden Semi Markov Models for Multiple Observation Sequences: The mhsmm Package for R.
Journal of Statistical Software, 39(4), 1-22.

Phylonium 1.4 – Fast and Accurate Estimation of Evolutionary Distances

Phylonium 1.4

:: DESCRIPTION

Phylonium is a program for estimating the evolutionary distances between closely related genomes. It is much faster than alignment based approaches for phylogeny reconstruction and usually more accurate than competing alignment-free methods.

::DEVELOPER

Fabian Klötzl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Phylonium

:: MORE INFORMATION

Citation

Klötzl F, Haubold B.
Phylonium: fast estimation of evolutionary distances from large samples of similar genomes.
Bioinformatics. 2020 Apr 1;36(7):2040-2046. doi: 10.1093/bioinformatics/btz903. PMID: 31790149; PMCID: PMC7141870.

FastEPRR 2.0 – Fast Estimation of Population Recombination Rates

FastEPRR 2.0

:: DESCRIPTION

FastEPRR is an extremely fast open-source software package to estimate population recombination rate based on intraspecific DNA polymorphism data.

::DEVELOPER

Evolutionary Genomics Lab, PICB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 FastEPRR

:: MORE INFORMATION

Citation

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era.
Gao F, Ming C, Hu W, Li H.
G3 (Bethesda). 2016 Mar 30. pii: g3.116.028233. doi: 10.1534/g3.116.028233

MPFE 1.28.0 – Estimation of Methylation Pattern Distribution from Deep Sequencing data

MPFE 1.28.0

:: DESCRIPTION

MPFE is an R Bioconductor package for calculation of the estimated distribution over methylation patterns.

::DEVELOPER

Peijie Lin, Sylvain Foret, Conrad Burden <conrad.burden at anu.edu.au>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 MPFE

:: MORE INFORMATION

Citation

Estimation of the methylation pattern distribution from deep sequencing data.
Lin P, Forêt S, Wilson SR, Burden CJ.
BMC Bioinformatics. 2015 May 6;16(1):145.

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