Kussell Lab at New York University
We combine theoretical biophysical approaches with experiments and bioinformatics to explore systems that exhibit complex, population-level phenomena.
12 Waverly Place, New York, 10003
Pinned Repositories
biogo
ecological-memory
hgtlib
forward population simulations with selection and recombination
mcorr
Inferring bacterial recombination rates from large-scale sequencing datasets.
mcorr-clustering
Hierarchical clustering using mcorr
PangenomeAlignmentGenerator
Align SRAs to pangenome FASTA file generated by Roary
popsimu
A GO package for population simulation with horizontal gene transfer
ReferenceAlignmentGenerator
Mapping reads to the reference genome to construct consensus genomes and generate alignments
viral-mcorr
Using correlated substitutions to infer recombination rates in RNA viruses
viral-mcorr_sl-cov_examples
Example workflows for using viral-mcorr to infer recombination rates for RNA viruses
Kussell Lab at New York University's Repositories
kussell-lab/mcorr
Inferring bacterial recombination rates from large-scale sequencing datasets.
kussell-lab/viral-mcorr
Using correlated substitutions to infer recombination rates in RNA viruses
kussell-lab/ReferenceAlignmentGenerator
Mapping reads to the reference genome to construct consensus genomes and generate alignments
kussell-lab/hgtlib
forward population simulations with selection and recombination
kussell-lab/PangenomeAlignmentGenerator
Align SRAs to pangenome FASTA file generated by Roary
kussell-lab/popsimu
A GO package for population simulation with horizontal gene transfer
kussell-lab/biogo
kussell-lab/ecological-memory
kussell-lab/go-misc
kussell-lab/Helicobacter_pylori_global_population
An example for mcorr
kussell-lab/mcorr-clustering
Hierarchical clustering using mcorr
kussell-lab/viral-mcorr_sl-cov_examples
Example workflows for using viral-mcorr to infer recombination rates for RNA viruses
kussell-lab/virus_alignment_example
Example workflow for aligning viral genomes for use with viral-mcorr using sars-like coronaviruses
kussell-lab/AssemblyAlignmentGenerator
Generating core-gene alignments from assemblies.
kussell-lab/bamfilter
Bam file filter
kussell-lab/Helicobacter_pylori_transformation_experiments
An example for mcorr
kussell-lab/hts
biogo high throughput sequencing repository
kussell-lab/mcorr_examples
Example data for mcorr
kussell-lab/ncbiftp