Pinned Repositories
GrapeTree
GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
BlastFrost
EToKi
all methods related to Enterobase
KleTy
KleTy: Klebsiella genotyping for its core genome and plasmids
PEPPAN
Phylogeny Enhanded Prediction of PAN-genome
PEPPAN_data
pHierCC
Hierarchical clustering of cgMLST
SimPan
A simulator of pan-genome for bacterial population
SPARSE
Strain Prediction and Analysis with Representative SEquence
StrTrak
StrTrak: Strain Tracker for metagenomic data
zheminzhou's Repositories
zheminzhou/EToKi
all methods related to Enterobase
zheminzhou/PEPPAN
Phylogeny Enhanded Prediction of PAN-genome
zheminzhou/SPARSE
Strain Prediction and Analysis with Representative SEquence
zheminzhou/pHierCC
Hierarchical clustering of cgMLST
zheminzhou/KleTy
KleTy: Klebsiella genotyping for its core genome and plasmids
zheminzhou/StrTrak
StrTrak: Strain Tracker for metagenomic data
zheminzhou/SimPan
A simulator of pan-genome for bacterial population
zheminzhou/cgMLSA
zheminzhou/OralMicrobiome
zheminzhou/PEPPAN_data
zheminzhou/BioData
All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
zheminzhou/biopython
Official git repository for Biopython (originally converted from CVS)
zheminzhou/BlastFrost
zheminzhou/BlastFrostSNP
Use BlastFrost to identify QRDR SNPs
zheminzhou/diverseClust
A simple script that can efficiently cluster divergent amino acid sequences based on the coverage of their alignments
zheminzhou/EPHI
Efficient Population History Inference
zheminzhou/fastSource
Accurate classification of bacterial source metadata based on FastText
zheminzhou/GrapeTree
zheminzhou/GrapeTree_tmpData
zheminzhou/kmer-db
zheminzhou/Li-et-al.-A.-baumanii-data-repo
zheminzhou/metaParser
Assign metadata into defined categories
zheminzhou/misc
zheminzhou/PhageBoost
Rapid discovery of novel prophages using biological feature engineering and machine learning
zheminzhou/public_kssd
K-mer substring space decomposition
zheminzhou/rapidNJ
Fast implementation of the Neighbour-Joining method for phylogenetic inference
zheminzhou/redHMM
RecHMM + DivHMM, identification of recombination and diversifying selection in bacterial genomes
zheminzhou/SRAdownload
A simple tool that downloads SRA short reads from either NCBI or EBI and converts them into fastq.gz files
zheminzhou/TemporalCurve
The script is designed as part of the supplementary data for the manuscript: https://www.biorxiv.org/content/early/2017/02/03/105759
zheminzhou/zscripts