All scripts can be downloaded from my Github page here. I have been working a lot on scripts for our new P2C2M R package, which will be posted after the package is finished and published (It will include both R and Python scripts)

 

R Scripts

 

structure.resampler

Subsamples a user-specified number of individuals per population and number of loci for mtDNA, microsatellite, or SNP datasets. Subsampled datasets are analysed by an AMOVA, pairwise Fst comparisons, and Exact Test in Arlequin. This is repeated for a user-specified number of replicates, and then the values are summarized across replicates.

 

write2arl

Converts microsatellite, SNP or mitochondrial sequence datasets (.csv format) to Arlequin format (.arp)

 

bamlist

Creates a bam.list from a folder of zipped fastq files for use with NGS pipelines, specifically those using GATK. Also creates a sample list.

 

 

Python Scripts

 

Python Scripts coming soon!