pamorin Goto Github PK

biogeobears-phylogeography

Scripts for using the BioGeoBears for phylogeographic model selection and inference.

change-taxa-names

R-scripts to change taxa names in Fasta or tree (NEWICK) files

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.

genome-wide_heterozygosity_gatk4

GATK4 pipeline to detect heterozygotes and assess heterozygosity in non-overlapping windows across scaffolds

genome_wide_heterozygosity_angsd

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

hwe_ld_jack_tests

Multi-test corrected tests for LD and HWE, with jackknife analysis to ID genotypes affecting HWE.

ibd

Isolation by distance (IBD) analyses for population genetic data.

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

psmc_boostrap_231122

Generate consensus diploid genome and run PSMC plus boostrap

snpdiscovery

Scripts for Methods in Molecular Biology chapter on SNP discovery

spca

R Markdown scripts for spatial PCA (sPCA) analysis of genotype data

stratag

strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

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

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.

tess3r_snps

R-markdown script for geographic population genetic structure analysis with Tess3r

vcfsnp_processing

visualization and re-calling of SNPs from vcf file