Phillip Morin's repositories
TESS3r_SNPs
R-markdown script for geographic population genetic structure analysis with Tess3r
SNPdiscovery
Scripts for Methods in Molecular Biology chapter on SNP discovery
BioGeoBears-phylogeography
Scripts for using the BioGeoBears for phylogeographic model selection and inference.
Demerelate_SNPs
Convert SNP and/or microhaplotype data to numerical input format, conduct "loci test" to determine number of loci needed for estimating relatedness, and estimate relatedness within demes.
HWE_LD_Jack_tests
Multi-test corrected tests for LD and HWE, with jackknife analysis to ID genotypes affecting HWE.
PSMC_boostrap_231122
Generate consensus diploid genome and run PSMC plus boostrap
Structure_Clumpp_Spatial_mapping_R
Rmarkdown scripts and test files for running STRUCTURE analysis, combining replicates with CLUMPP, and generating assignment barplots and spatial interpolation of ancestry coefficient
Change-taxa-names
R-scripts to change taxa names in Fasta or tree (NEWICK) files
Genome-wide_heterozygosity_GATK4
GATK4 pipeline to detect heterozygotes and assess heterozygosity in non-overlapping windows across scaffolds
Get_SRA_files_for_BioProject
Uses SRAtoolkit functions to obtain information on all SRR files in a BioProject at NCBI, then download them to the current directory
Microhaplotype_processing
visualization and re-calling of microhaplotypes from unfiltered Microhaplot output
Microhaplotype_Remove_N_alleles
removes loci with more than specified percent of N's in haplotypes (based on Microhaplot output)
Mitogenome_taxonomy
Scripts used for population, subspecies, and species mitogenome divergence and simulations
Pie-charts-on-map
plot pie charts of frequencies on map at specified locations
strataG
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
Target_SNP_vcf_filter_transform
Scripts in R-markdown to transform vcf data for single SNPs into data for visualization and filtering prior to analysis.
vcfSNP_processing
visualization and re-calling of SNPs from vcf file