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[Parsnp 2]
Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ:
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets.
bioRxiv (2024). doi: https://doi.org/10.1101/2024.01.30.577458
[Parsnp 1]
Treangen TJ*, Ondov BD*, Koren S, Phillippy AM:
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
Genome Biology (2014). doi: http://dx.doi.org/10.1186/s13059-014-0524-x
* These authors contributed equally to this work
External software (please also cite if you find Parsnp useful):
[FastTree2]
Price MN, Dehal PS, Arkin AP:
FastTree 2--approximately maximum-likelihood trees for large alignments.
PLoS One 2010, 5:e9490.
[Muscle]
Edgar RC:
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic Acids Research 2004, 32:1792-1797.
[PhiPack]
Bruen TC, Philippe H, Bryant D:
A simple and robust statistical test for detecting the presence of recombination.
Genetics 2006, 172:2665-2681.
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