Tag: Statistical

EuroForMix 3.3.3 – Statistical DNA Interpretation

EuroForMix 3.3.3

:: DESCRIPTION

EuroForMix is an advanced fully validated open-source, free software used to interpret complex DNA profiles (mixtures) taking into account peak height, stutter and degradation.

::DEVELOPER

EuroForMix team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

EuroForMix

:: MORE INFORMATION

Citation

Pascali VL.
A novel computational strategy to predict the value of the evidence in the SNP-based forensic mixtures.
PLoS One. 2021 Oct 15;16(10):e0247344. doi: 10.1371/journal.pone.0247344. PMID: 34653182; PMCID: PMC8519470.

Topali 2.5 r3 – Statistical & Evolutionary Analysis of Multiple Sequence Alignments

Topali 2.5 r3

:: DESCRIPTION

Topali (tree TOPology-related analysis of ALignments Interface) is a software for statistical and evolutionary analysis of multiple sequence alignments.The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Topali

:: MORE INFORMATION

Citation

Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF and Wright F (2008),
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops,
Bioinformatics 25 (1), 126-127.

GemIdent 2.1 – Statistical Image Segmentation System

GemIdent 2.1

:: DESCRIPTION

GemIdent is an interactive program that identifies regions of interest in images. It is specifically designed for color segmentation in images with few colors, where the objects of interest look alike with small variation.

::DEVELOPER

Dr. Adam Kapelner in the lab of Dr. Peter Lee under the tutelage of Professor Susan Holmes.

:: SCREENSHOTS

GemIdent

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 GemIdent

:: MORE INFORMATION

Citation

J Stat Softw. 2009 Jun 1;30(10). pii: i10.
An Interactive Java Statistical Image Segmentation System: GemIdent.
Holmes S, Kapelner A, Lee PP.

ViSEN 1.0beta0.3 – Visualization tool for Statistical Epistasis Networks

ViSEN 1.0beta0.3

:: DESCRIPTION

ViSEN provides a graphical visualization for statistical epistasis.  Pairwise and three-way epistatic interactions are measured using information gain and are represented using networks.

::DEVELOPER

ViSEN team

:: SCREENSHOTS

ViSEN

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 ViSEN

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Apr;37(3):283-5. doi: 10.1002/gepi.21718. Epub 2013 Mar 6.
ViSEN: methodology and software for visualization of statistical epistasis networks.
Hu T, Chen Y, Kiralis JW, Moore JH.

SWAN 0.3.0 – Statistical Structural Variation ANalyzer

SWAN 0.3.0

:: DESCRIPTION

SWAN is the first to introduce a statistically verifiable heterogeneity SV model to the community. As in SWAN, the genetic material sampled is no longer viewed as a homogenous mutant or reference sample but explicitly modeled as a mixture of both mutant and reference sequences with their fractions estimable.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

SWAN

:: MORE INFORMATION

Citation

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
LC Xia, S Sakshuwong, E Hopmans, J Bell, S Grimes, D Siegmund, H Ji, Nancy Zhang.
Nucleic Acids Research 44 (15), e126 (2016)

BioStat 5.3.0 – Biology Statistical Software

BioStat 5.3.0

:: DESCRIPTION

BioStat is a user-friendly biology and medicine oriented statistical software.With BioStat 2009, one gets a robust suite of statistics tools and graphical analysis methods that are easily accessed though a simple and straightforward interface.

::DEVELOPER

AnalystSoft Inc

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BioStat

:: MORE INFORMATION

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