MatCompare 1.3 – Compare Transcription Factor Binding Site (TFBS) position Frequency Matrices (PFMs)

MatCompare 1.3

:: DESCRIPTION

The MatCompare software provides methods for comparing transcription factor binding site (TFBS) position frequency matrices (PFMs). The user has a choice of using the Kullback-Leibler divergence, the chi squared test or the Fisher-Irwin exact test of similarity.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 MatCompare

:: MORE INFORMATION

Citation:

Dustin E Schones, Pavel Sumazin and Michael Q Zhang
Similarity of position frequency matrices for transcription factor binding sites
Bioinformatics 2005 21(3):307-313; doi:10.1093/bioinformatics/bth480

MultiGlycan 1.0 – Annotation of Glycomic Profiles in the LC-MS data

MultiGlycan 1.0

:: DESCRIPTION

MultiGlycan helps user to gather glycan profile information from LC-MS Spectra. It also reports quantity of specific glycan composition.

::DEVELOPER

Haixu Tang

:: SCREENSHOTS

MultiGlycan

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MultiGlycan

 :: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1706-7. doi: 10.1093/bioinformatics/btt190. Epub 2013 Apr 22.
Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry.
Yu CY1, Mayampurath A, Hu Y, Zhou S, Mechref Y, Tang H.

BetaScan 2 – Genome-wide Scan for Balancing Selection using Beta Statistic

BetaScan 2

:: DESCRIPTION

BetaScan is designed to calculate Beta, a summary statistic for the frequency spectrum (similar to Fay and Wu’s H, or Taajima’s D) sensitive to the signature of balancing selection.

::DEVELOPER

Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

BetaScan

:: MORE INFORMATION

Citation:

Siewert KM, Voight BF.
BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data.
Genome Biol Evol. 2020 Feb 1;12(2):3873-3877. doi: 10.1093/gbe/evaa013. PMID: 32011695; PMCID: PMC7058154.

CERVUS 3.0.7 – Parentage Analysis

CERVUS 3.0.7

:: DESCRIPTION

Cervus is the software package for parentage analysis in plant and animal populations. It combines a robust likelihood-based method with a simple graphical interface.

Cervus is a computer program for assignment of parents to their offspring using genetic markers.

Cervus uses likelihood, a well-established statistical method for parentage analysis, to assign parentage. Cervus introduces two key enhancements to this process:
1) Likelihood ratios are calculated allowing for the possibility that the genotypes of parents and offspring may be mistyped.
2) Cervus determines via simulation the level of confidence in the parentages it assigns.

Cervus represents an easy-to-use and practical tool for scientists seeking to establish parent-offspring relationships even when some genotypes are incomplete, incorrect or missing.

::DEVELOPER

Field Genetics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Cervus

:: MORE INFORMATION

Citation

Mol Ecol. 2007 Mar;16(5):1099-106.
Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.
Kalinowski ST1, Taper ML, Marshall TC.

MetalDetector 2.0 – Cysteines and Histidines Binding State Predictor

MetalDetector 2.0

:: DESCRIPTION

MetalDetector identifies cysteines and histidines involved in transition metal protein binding sites, starting from the protein sequence alone.

::DEVELOPER

MetalDetector team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W288-92. doi: 10.1093/nar/gkr365. Epub 2011 May 16.
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence.
Passerini A, Lippi M, Frasconi P.

bcfind 1.0 – Brain cell finder

bcfind 1.0

:: DESCRIPTION

bcfind is a tool for fully automated localization of soma in 3D mouse brain images acquired by confocal light sheet microscopy.

::DEVELOPER

bcfind team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Sep 1;30(17):i587-i593. doi: 10.1093/bioinformatics/btu469.
Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images.
Frasconi P, Silvestri L, Soda P, Cortini R, Pavone FS, Iannello G.

ICDMR – Identification of Consistently Differentially Methylated Regions

ICDMR

:: DESCRIPTION

ICDMR is an unsupervised approach, where there is no need to choose the comparative group in advance, and is able to identify methylation modifications either among individuals or between potential subgroups in a population.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 ICDMR

:: MORE INFORMATION

Citation

A novel method for identification and quantification of consistently differentially methylated regions.
Hsiao CL, Hsieh AR, Lian IeB, Lin YC, Wang HM, Fann CS.
PLoS One. 2014 May 12;9(5):e97513. doi: 10.1371/journal.pone.0097513

WHAMM 0.14c – Whole-Genome Homozygosity Analysis and Mapping Machina

WHAMM 0.14c

:: DESCRIPTION

WHAMM is a free, open-source analysis package designed to estimate patterns of homozygosity in whole genome data sets, as well as perform a range of association analyses and summaries on the resultant output.

::DEVELOPER

Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   WHAMM

:: MORE INFORMATION

iHS_calc 1.4 – Calculate the Integrated Hapotype Score

iHS_calc 1.4

:: DESCRIPTION

iHS_calc is designed to calculate the integrated Hapotype Score (iHS).

::DEVELOPER

Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  iHS_calc

:: MORE INFORMATION

Citation:

PLoS Biol. 2006 Mar;4(3):e72. Epub 2006 Mar 7.
A map of recent positive selection in the human genome.
Voight BF1, Kudaravalli S, Wen X, Pritchard JK.

MR_predictor 0.028 – A Simulation Engine for Mendelian Randomization Studies

MR_predictor 0.028

:: DESCRIPTION

MR_predictor is a free, open-source simulation engine designed to guide the development and interpretation of statistical tests of causality between phenotypes using genetic instruments.

::DEVELOPER

Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MR_predictor

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Aug 26. pii: btu564.
MR_predictor: a simulation engine for Mendelian Randomization studies.
Voight BF.