Tutorials

Genomics

How to install R and Rstudio under Ubuntu Linux version 20.04

How to convert between a PHYLIP file and FASTA file, and how to convert from a FASTA file to a Nexus file

How to make an Arlequin file from a FASTA file

How to perform an alignment for mitochondrial or plastid DNA sequences

How to do an Analysis of Molecular Variance (AMOVA) using Arlequin

How to get the pairwise FST information out of Arlequin into more convenient formats

How to do a Spatial Analysis of Molecular Variance (SAMOVA)

How to perform a mantel test comparing genetic distances to geographic distances using R

How to make a STRUCTURE file from a FASTA file

A brief overview of the program STRUCTURE for population genetic analysis

See the show notes on YouTube for the links referenced in the video

How to perform Bayesian clustering analysis using the program STRUCTURE

How to decide which results from STRUCTURE to use

How to perform a QTL analysis using the qtl package in R and plot the results

How to perform a QTL power analysis using R

How to most easily visualize the results from STRUCTURE and make a publication-ready figure

How to test for the correct nucleotide substitution model using jmodeltest2

How to install the population genetic software PartitionFinder under Ubuntu Linux version 20.04

How to install the population genetic software jModelTest2 under Ubuntu Linux version 20.04.

How to convert an output file from MrBayes, which is in Nexus format, into the Newick tree file format for making phylogenies.

How to perform a Bayesian Markov Chain Monte Carlo (MCMC)-based phylogenetic analysis using the software MrBayes.

How to perform phylogenetically independent contrasts

How to install the R package 'phytools' under Ubuntu Linux version 20.04. 

How to install the R package 'pegas' under Ubuntu Linux version 20.04. 

How to make a publication-ready phylogeny figure using R and Inkscape (advanced)

How to install fastStructure on Ubuntu Linux 20.04

How to install and run STRUCTURE under Ubuntu Linux 20.04

How to install distruct on Ubuntu Linux 20.04

How to hook up and use my pre-configured Ubuntu Linux virtual machine on your Windows computer

How to hook up and use my pre-configured Ubuntu Linux virtual machine on your Mac computer

Geographic Information Systems (GIS)

Tutorials using ArcGIS 

How to perform logistic regression with correction for spatial autocorrelation

How to export a points layer from ArcGIS as a shapefile so that you can send it to someone else

Tutorials using R

How to get the highest resolution hydrology data for your area of interest within the US and to create GIS layers from it

How to extract raster values (from Maxent or elsewhere) at point locations using R

Tutorials using GRASS GIS

Introduction to GIS and GRASS GIS

See the show notes for the links mentioned in the video.

Projections, transformations, and GPS data import

Rasters and raster manipulation

Buffering and clipping vectors

Tutorials for doing cartography using QGIS

Species Distribution Modeling

How to install the R Package 'ENMEval' (and 'xml2,' 'tidyverse,' 'rJava') under Ubuntu Linux 20.04

How to install the R Package 'ENMTools' under Ubuntu Linux 20.04

How to adjust your environmental layers so that they have exactly the same spatial extent and resolution

How to check for correlations among environmental layers and remove ones that are highly correlated (using ENMTools in R)

How to install the the R package RMark, as well as the mark-recapture program Mark, on the Ubuntu Linux operating system

How to use the mark-recapture program Mark under R (by using the RMark package)

How to decide which settings to use when running Maxent, as well as how to make a bias file

How to perform species distribution modeling using Maxent

How to make publication-quality figures of response curves from the Maxent output

How to test whether two species distribution models are significantly different from each other (using ENMTools in R)

How to install the stand-alone version of ENMTools under Ubuntu Linux 20.04