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Welcome to the PALM wiki!

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Announcements

• 05/20/2020: Please see new documentation for Relate v1.1. The output format of SampleBranchLengths has changed, which has streamlined the process of running PALM (and CLUES) on Relate-inferred trees.
• 05/06/2020: Documentation is still in development. Please raise issues here on GitHub (rather than my email) if you have any suggestions or run into any issues.

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At a glance

PALM (Polygenic Adaptation Likelihood Method) is a method for estimating & testing adaptation of complex traits using a combination of population genetic data and GWAS summary statistics.

Broadly, PALM relies on two types of data:

• Genealogies/coalescence times at SNPs/markers of interest
• GWAS summary statistics (sumstats)

The typical pipeline for running PALM looks like this, at a glance:

1. Get coalescence times for SNPs/markers
2. Calculate SNP likelihoods using lik.py (these are functions of s, the selection coefficient of the SNP)
3. Format sumstats and organize files for PALM.
4. Run PALM on likelihoods + GWAS using palm.py

Example trait metadata/sumstats & SNP likelihoods can be downloaded from

https://datadryad.org/stash/share/7adGHKARPRTcQm3ZvkIXV0EmCCORArxu83M7LKWl1E0

(These are useful to follow some of the later tutorial steps)

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If you use this software in published work, please cite:

• Stern AJ, et al., bioRxiv (2020), https://doi.org/10.1101/2020.05.07.083402

And also

• Stern AJ, et al., PLOS Genetics (2019), https://doi.org/10.1371/journal.pgen.1008384
• Speidel L, et al., Nature Genetics (2019), https://doi.org/10.1038/s41588-019-0484-x