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Soochow University
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SPARSE Public
Strain Prediction and Analysis with Representative SEquence
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EToKi Public
all methods related to Enterobase
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KleTy Public
KleTy: Klebsiella genotyping for its core genome and plasmids
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StrTrak Public
StrTrak: Strain Tracker for metagenomic data
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pHierCC Public
Hierarchical clustering of cgMLST
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redHMM Public
RecHMM + DivHMM, identification of recombination and diversifying selection in bacterial genomes
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SRAdownload Public
A simple tool that downloads SRA short reads from either NCBI or EBI and converts them into fastq.gz files
Python GNU General Public License v3.0 UpdatedMay 31, 2022 -
rapidNJ Public
Forked from somme89/rapidNJFast implementation of the Neighbour-Joining method for phylogenetic inference
C++ GNU General Public License v2.0 UpdatedFeb 10, 2022 -
BioData Public
Forked from bjtully/BioDataAll of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
Python MIT License UpdatedAug 31, 2021 -
PhageBoost Public
Forked from ku-cbd/PhageBoostRapid discovery of novel prophages using biological feature engineering and machine learning
Jupyter Notebook GNU General Public License v3.0 UpdatedJul 27, 2021 -
public_kssd Public
Forked from yhg926/public_kssdK-mer substring space decomposition
C Other UpdatedJun 10, 2021 -
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biopython Public
Forked from biopython/biopythonOfficial git repository for Biopython (originally converted from CVS)
Python Other UpdatedDec 26, 2020 -
PEPPAN Public
Phylogeny Enhanded Prediction of PAN-genome
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kmer-db Public
Forked from refresh-bio/kmer-dbC++ GNU General Public License v3.0 UpdatedJul 1, 2020 -
BlastFrost Public
Forked from nluhmann/BlastFrostC++ GNU General Public License v3.0 UpdatedJun 27, 2020 -
fastSource Public
Accurate classification of bacterial source metadata based on FastText
Python GNU General Public License v3.0 UpdatedJun 22, 2020 -
GrapeTree Public
Forked from achtman-lab/GrapeTreeJavaScript GNU General Public License v3.0 UpdatedJun 8, 2020 -
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SimPan Public
A simulator of pan-genome for bacterial population
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BlastFrostSNP Public
Use BlastFrost to identify QRDR SNPs
Python GNU General Public License v3.0 UpdatedFeb 21, 2020 -
diverseClust Public
A simple script that can efficiently cluster divergent amino acid sequences based on the coverage of their alignments
Python GNU General Public License v3.0 UpdatedNov 25, 2019 -
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TemporalCurve Public
The script is designed as part of the supplementary data for the manuscript: https://www.biorxiv.org/content/early/2017/02/03/105759
Python UpdatedJan 30, 2018