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203.328

Module 6 Lab Resources – Genome Analysis 203.328

2d_fir_distribution

Code to calculate 5ʹ and 3ʹ distances to the nearest gene

3d_contact_distribution

Code to calculate 3D contact distributions for subsets of genes

admixture_estimator

adwave

Wavelet analysis of genomic data from admixed populations

asiamodel

Testing site for msprime coalescent models of Asian demography

bali_lattice

Javascript Bali lattice model

drifter

Simulate genetic drift and sampling error in population genetic samples

fasta_select

Extract specified sequences from a fasta file

filter_fasta

Filter fasta sequences by size

filtfst

filtFst calculates Fst, a measure of population differentiation due to genetic structure

frequency_diff

Calculate probability of allele frequency differences by resampling

gene_ordering

Code to simulate random gene loss in the yeast genome

gst_prime

Implementation of a standardized genetic differentiation measure

hapmatch

Determines lineages with given ingroup and outgroup frequencies in coalescent genealogies

hybridrnasim

Simulating 'neutral' gene expression patterns in hybrids and their progenitors

imgc

Finds the largest non-recombining block in a DNA alignment

lesson-example

Example lesson using The Carpentries lesson template.

mapcount

Counts read hits against a reference gene set

microsat

Microsat simulates the evolution of linked and unlinked microsatellites using the coalescent.

models

Models for website hosting

monte

Statistical significance of high and low mutation rates

msrho

Calculates the rho statistic for coalescent genealogies

mstree

Calculates TMRCA and the minimum clade proportion for coalescent genealogies

recomb

The recomb package simulates and summarizes genetic datasets with recombination rates that change over time.

seqstats

Calculate sequence statistics of fasta files

summarize_contigs

Characterize contigs in a fasta file, including telomere information

update

Automate Linux updates