Here you'll find the code associated with the paper:
Ament-Velásquez et al. (2025) Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing (under review)
Here I have three pipelines in different folders:
- HNWDphylogeny: Small pipeline (
HNWDphylogeny.smk) to produce maximum likelihood phylogenies of different parts of an NWD protein alignment. (The actual figure in the paper was put together in Inkscape). - JustHetGenes: contains the pipeline
HETwd40explorer.smk, more or less as in the bioRxiv version. Here we compare assemblies, alleles, and WD40 repeats of het-d, het-e, and het-r. Most figures in the paper come from here. - NWDgenes: contains the pipeline
NWD40explorer.smk, which extends the pipeline above to all NWD genes with HIC WD40 repeats. Here we produced the LOGO and PCA analysis.
They are all Snakemake pipelines that more or less depend on conda environments for plotting.
Disclaimer: These scripts and files are provided "as is" and without any express or implied warranties, including, without limitation, the implied warranties of merchantability and fitness for a particular purpose.