pyani
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Contents:
Citing
pyani
About
pyani
QuickStart Guide
Requirements
Installation Guide
Basic Use
Downloading Genomes from NCBI
Indexing Genomes
Creating a Local
pyani
Database
Running ANIm analysis
Interpreting the Graphical Output
Examples
pyani
subcommands
Use With a Scheduler
Testing
Contributing to
pyani
Licensing
pyani package
pyani
Docs
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Basic Use
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Basic Use
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Contents:
Downloading Genomes from NCBI
Download all genomes in a single taxon
Download all genomes from multiple taxa
Dry-run test (identify, but do not download, files)
Download genomes for compilation of a custom
Kraken
database
Indexing Genomes
What does indexing do?
Index a directory of FASTA files
Creating a Local
pyani
Database
Create a new empty
pyani
database
Create an empty
pyani
database at a specific location
Running ANIm analysis
Perform ANIm analysis
Perform ANIm analysis with Open Grid Scheduler
References
Interpreting the Graphical Output
The Output
Heatmaps
Distribution Plots
Scatterplots
Plot Asymmetry
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