laninsky Goto Github PK

2018-08-24-otago

ambigoos_into_structure

Taking fasta alignments with ambiguity codes and turning them into a structure file

bats_and_rats

Analyses corresponding to Mindanao PAIC bats and rats diversification project

beetles

Analysis code used for various beetle UCE projects

ceyx

Analyses related to RADseq study on Ceyx

chickadees

Analyses and data corresponding to "Limited movement of a hybrid zone in relation to regional variation in magnitude of climate change"

combining_samples_from_structure

Combining technical replicates/replicate samples at the structure file stage

comparing_monolithic_uce_fastas

Blasting between monolithic UCE fasta files to find out which loci are shared between different base genomes

constructing_allelic_ladder

Given a list of samples that can be used to construct the allelic ladder, this script will give a selection of samples that cover alleles found in the greater population

correlating_cladogenesis_with_periodic_things

creating_dadi_snp_input_from_structure

Do you want to chuck your SNPs through dadi, but are coming from stacks/structure? This script might help

direct_mito_sequencing

distance_calcs

Calculates pairwise distance between samples for a folder of fasta files

divergent_allele_test

Are the combination of alleles in your population the most divergent you could get out of the alleles in the total meta-population?

easter-birthdays

Some quick R code to find out which years your birthday overlaps Easter

edm

demonstration empirical dynamic modeling code

finding_loci_based_off_primers

Uses BLAST and R scripts to find genomic position of loci based off their primer sequences and expected size

frogs

Analysis code used on various UCE frog papers

fst_dxy

Inherited a STACKs dataset consiting of the sumstats.tsv and catalog.tags.tsv files? This will create a fasta file per locus

gbs_snp_filter

filtering SNPs based on LD and HWE status

genetic_diversity_diffs

Tests for significant differences in genetic diversity between populations based on DNA sequence data

genome-scripts

Some hodge podge scripts for dealing with genome stuff

github_admin

digital lab book example

github_and_rstudio

hierfstat_by_pop

Using hierfstat to get per population overall FIS values

instructor-training

Software and Data Carpentry instructor training course material

laninsky.github.io

making_migrate_files

Assembling fasta and SNP data into a file that can be inputted into migrate

missing_data_for_uce_loci

Need to figure out the average amount of missing data per sample across your UCE loci? Look no further!

model_pcr_error