Tag: Pathogen

PathoGiST v0.3.6 – Clustering Pathogen Isolates by combining multiple Genotyping Signals

PathoGiST v0.3.6

:: DESCRIPTION

PathOGiST is an algorithmic framework for clustering bacterial isolates by leveraging multiple genotypic signals and calibrated thresholds.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda

:: DOWNLOAD

PathOGiST

:: MORE INFORMATION

Citation

Katebi M. et al. (2020)
PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals.
Algorithms for Computational Biology. AlCoB 2020. Lecture Notes in Computer Science, vol 12099. Springer, Cham. https://doi.org/10.1007/978-3-030-42266-0_9

TransPhylo 1.45 – Inference of Pathogen Transmission Tree given Phylogeny

TransPhylo 1.45

:: DESCRIPTION

TransPhylo is a software package for the Bayesian inference of infectious disease transmission from a phylogeny.

::DEVELOPER

Xavier Didelot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 TransPhylo

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 Jul;31(7):1869-79. doi: 10.1093/molbev/msu121. Epub 2014 Apr 8.
Bayesian inference of infectious disease transmission from whole-genome sequence data.
Didelot X, Gardy J, Colijn C

DetectiV 1.2 – Analysis of Pathogen Detection Microarray data

DetectiV 1.2

:: DESCRIPTION

DetectiV is a package for R containing functions for visualisation, normalisation and significance testing of pathogen detection microarray data. DetectiV uses simple and established methods for visualisation, normalisation and significance testing. When applied to a publicly available microarray dataset, DetectiV produces the correct result in 55 out of 56 arrays tested, an improvement on previously published methods.

::DEVELOPER

Michael Watson 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R Package

:: DOWNLOAD

 DetectiV

:: MORE INFORMATION

Citation:

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data.
Watson M, Dukes J, Abu-Median AB, King DP, Britton P.
Genome Biol. 2007;8(9):R190.

WKL – Pathogen Detection Algorithm

WKL

:: DESCRIPTION

WKL (weighted Kullback-Leibler divergence) is a program that identifies viruses presented in a pathogen chip by analyzing and differentiating their signal intensity distribution with the background signal intensity distribution.

:: DEVELOPER

Genome Institute of Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 WKL

:: MORE INFORMATION

Citation

Genome Biol. 2007;8(5):R93.
Optimization and clinical validation of a pathogen detection microarray.
Wong CW, Heng CL, Wan Yee L, Soh SW, Kartasasmita CB, Simoes EA, Hibberd ML, Sung WK, Miller LD

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