Cutoff Finder v1 – Determination of Cutoff Points in Molecular data

Cutoff Finder v1

:: DESCRIPTION

Cutoff Finder is an easy–to–use web application for the determination of cutoff points in molecular data. Often, molecular data such as gene expression or protein expression data are represented by continuous or at least ordinal variables. In order to translate these variables into a clinical decision, it is necessary to determine a cutoff point and to stratify patients into two groups, each of which requiring a different kind of treatment. Cutoff Finder offers a multitude of methods for cutoff determination and plots.

::DEVELOPER

Cutoff Finder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(12):e51862. doi: 10.1371/journal.pone.0051862. Epub 2012 Dec 14.
Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization.
Budczies J1, Klauschen F, Sinn BV, Győrffy B, Schmitt WD, Darb-Esfahani S, Denkert C.

SIMCOAL 2.1.2 – Simulation of Molecular data in interconnected Populations with Arbitrary Demography

SIMCOAL 2.1.2

:: DESCRIPTION

SIMCOAL (SIMulate COAlescence) is a computer program for the simulation of molecular genetic diversity in an arbitrary number of haploid populations examined for a set of fully linked loci.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SIMCOAL

:: MORE INFORMATION

Citation

Excoffier, Novembre, Schneider (2000),
SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography“,
Journal of Heredity, 91:506-509.

ADMIX 2.0 – Computing Admixture Coefficients from Molecular data

ADMIX 2.0

:: DESCRIPTION

The program Admix can be used to compute the estimators mY of admixture coefficients from molecular data initially described in Bertorelle & Excoffier (1998) and extended to any number of parental populations by Dupanloup & Bertorelle (2001).

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

n/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ADMIX

:: MORE INFORMATION

Citation

Mol Biol Evol (2001) 18 (4): 672-675.
Inferring Admixture Proportions from Molecular Data: Extension to Any Number of Parental Populations
Isabelle Dupanloup and Giorgio Bertorelle

TreeTime 1.0.1 – Bayesian Sampling of Phylogenetic Trees from Molecular data

TreeTime 1.0.1

:: DESCRIPTION

TreeTime is an extensible C++ software package for the Bayesian sampling of phylogenetic trees from molecular data.

::DEVELOPER

Lin Himmelmann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX

:: DOWNLOAD

 TreeTime

:: MORE INFORMATION

Citation

TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration.
Himmelmann L, Metzler D.
Bioinformatics. 2009 Sep 15;25(18):2440-1. doi: 10.1093/bioinformatics/btp417.

phyutility 2.6 – Phyloinformatic Utility for Trees, Alignments, and Molecular data

phyutility 2.6

:: DESCRIPTION

phyutility (Phyloinformatic utility) is a Java program to perform simple but essential tasks on sequences and trees from the command line.

::DEVELOPER

STEPHEN A. SMITH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 phyutility

:: MORE INFORMATION

Citation

Smith, S. A. and Dunn, C. W. (2008)
Phyutility: a phyloinformatics tool for trees, alignments, and molecular data.
Bioinformatics. 24: 715-716