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GENPAT (Italian National Reference Centre for WGS of microbial pathogens)'s Projects

cgmlst-dists icon cgmlst-dists

🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables

cgmlst-dists-64 icon cgmlst-dists-64

A fork of the cgmlst-dists program that has been modified to manage large files and uses 64-bit integers to calculate the size of distance vector.

cgmlst-dists-py icon cgmlst-dists-py

The python multithreaded version of the famous cgmlst-dists bioinformatic tool by Torsten Seemann

grapetree-gis icon grapetree-gis

Project based on GrapeTree, a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.

pairwisedifferencestoroc icon pairwisedifferencestoroc

Script performing Receiver Operating Characteristic (ROC) analysis to identify thresholds of mutation pairwise differences from microbial genomes involved in an investigated outbreak

spread icon spread

Project based on GrapeTree, a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata.

treetocongruency icon treetocongruency

Script comparing two trees through a tanglegram and estimations of congruency metrics

vcf2mst icon vcf2mst

Hamming Distance based Minimum Spanning Tree from Samples vcf using graptree

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