Resources (UNDER CONSTRUCTION ALWAYS)
R Resources
R studio download here
R Graph Gallery-useful resource for plotting nice figures in R here
Basic Stats and Visualization Tutorial R-Markdown here
PCA and plotting in R. R-Markdown here
ggtreeExtra package write-up here
A quick and dirty code for mining gene data from NCBI GenBank with taxid information here
A tutorial on phylogenetic tree simulation for trait simulation, character mapping, etc. here
A quick tutorial on making an ultrametric dated phylogeny in R here
A very introductory approach to R for early undergraduates here
A very introductory approach to subsetting data in R here
Coding Resources
Codewars (Improve coding skills by training with others on code challenges) here
replit--online IDE for team coding here
Sanbox.bio--interactive bioinformatics tutorials here
Rosalind--helpful for learning bioinformatics and programming here
w3 schools--Helpful info and tutorials on coding websites here
From R to Python--Helpful resources and links compiled to assist in learning Python with R background here
Databases
NCBI GenBank-NIH sequence database here
SRA (Sequence Read Archive)- largest publicly available repository of high throughput sequence data here
Animal Genome Size Database- Collection of genome size data curated by T. Ryan Gregory at University of Guelph here
Karyotype Databases- Collections of karyotypes for beetles, Polyneoptera, and amphibians, curated by Heath Blackmon at Texas A&M University here
Tree of Sex Database--Collections of sex chromosomes systems for many animals here
AlphaFold--Protein Structure Database here
Useful Websites and Tools
NCBI BLAST-Online nucleotide/protein sequence identity/alignment here
MAFFT Online-Online sequence alignments for phylogenetics here
Nextstrain- Real-time tracking of pathogen evolution here
NGPhylogeny--Automated workflow of simple phylogenies here
Genetics & Evolution Webtools here
Alliance of Genome Resources Tools and Prototypes here
BioRender--Professional Science Figures here
Phytools (Phylogenetic Tools for Comparative Biology) Blog here
Taming the BEAST-BEAST2 tutorial here
County lines map webiste--Use Lat/long info to find county information for Utah here
BioIcons--A free library of open source icons for scientific illustrations using vector graphics software such as inkscape or Adobe Illustrator here
PhyloPic--free silhouette images of animals, plans, and other life forms available for reuse here
EcoEvo Job board--Google Sheet with faculty and post doc job opportunities here
Useful Programs
R-program here
BAMM (Bayesian Analysis of Macroevolutionary Mixtures) program and documentation here
Simple population genetic simulations- by Heath Blackmon at Texas A&M University here
Brownian motion simulations- By Heath Blackmon at Texas A&M University here
Useful Papers and Articles
ALWAYS ADDING
"DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics" here
"Drosophila Evolution over Space and Time (DEST): A new population genomics resource" here
"How software in the Life Sciences actually works (and doesn't work)" here
SNPfiltR: an R package for interactive and reproducible SNP filtering
here
"Best Online Linux Terminals and Online Bash Editors" here
"Teaching Biology through Statistics: Application of Statistical Methods in Genetics and Zoology Courses" here