Databases:
- NCBI – National Center for Biotechnology Information
- GenBank – Nucleotide sequence database
- BOLD – Barcode of Life Data Systems database
- Ensembl Genome Browser
- dbSNP – Single nucleotide polymorphism database
- UCSC Genome Browser
- 1000 Genomes Project
- gnomAD – Genome Aggregation Database
- ALFRED – Allele Frequency Database
- Dryad – Open data repository for published datasets
- International Barcode of Life (iBOL) – Global biodiversity genomics consortium
Commonly Used:
- Arlequin – Population genetics analysis software
- Genepop – Population genetics software suite
- MEGA – Molecular Evolutionary Genetics Analysis software
- BioEdit – Biological sequence alignment editor for Windows
- TreeViewer – Flexible, modular phylogenetic tree visualization software
- TreeView X – Open‑source tree drawing software for phylogenetic trees
- FigTree – Graphical viewer and publication‑ready tree figure tool
- Clustal Omega – Multiple sequence alignment program using HMM‑based guide trees
- Gene Codes (Sequencher) – DNA sequencing analysis software suite
- R – Statistical computing environment
- RStudio – Integrated development environment for R
- PAST – Free statistical software for paleontological data
- Notepad++ – Free source code editor and Notepad replacement
- Python – High‑level, general‑purpose programming language with extensive scientific libraries
- SAP on GitHub – Assigns sequences to species via GenBank data
- SPAM (Statistics Program for Analyzing Mixtures) – admixture assignment software developed by the Alaska Department of Fish and Game’s Gene Conservation Laboratory
Additional Helpful Resources:
- Evolutionary Genetics Software Applications | AMNH – Collection of population‑genetics, evolution, and phylogenetics programs
- PLINK – Whole‑genome association and population‐based linkage analysis
- adegenet (R) – Multivariate analysis of genetic markers
- VCFtools – Utilities for Variant Call Format files
- TreeMix – Inferring population splits and mixtures
- Galaxy Project – Web‑based bioinformatics workflows
- Mesquite – Modular evolutionary biology software for phylogenetic and population‑genetics analysis
- PAUP* – Phylogenetic Analysis Using Parsimony and other methods
- PopART – Population Analysis with Reticulate Trees software – make haplotype networks
- BEAST – Bayesian evolutionary analysis sampling trees platform
- PAML – Phylogenetic Analysis by Maximum Likelihood package
- Geneious – Integrated bioinformatics software for sequence data analysis