Evolutionary Genetics Resources: Simulation, Population Genetics, and Phylogenetic Software
This is not an exhaustive list in no capacity. I created it as a reference for my lab as a good starting point. I wanted to thank Peter Beerli for sharing links to some of relevant course material.
Seven categories of simulation uses in molecular ecology
(i) infer species’ history, (ii) infer species’ biology, (iii) predict probable species’ response to environmental change (often for policy purposes), (iv) predict outcomes of possible management interventions (for choosing appropriate actions), (v) evaluate method performance, (vi) evaluate/optimize sampling strategy, (vii) explore models of complex processes to discover new phenomena (e.g. emergent properties) or develop theory.
Simulation tools
Simulating Adaptation

PEDAGOG is a Windows program that simulates population dynamics at the individual level, allows for heritability and selection of traits, records individual genotype and pedigree information

quantiNEMO An individualbased program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population

SLiM is a simulating evolution with selection and linkage
Simulating life history trait evolution

NEMO Individualbased, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history traits and population genetics in a spatially explicit, metapopulation framework
Coalescence

FASTSIMCOAL2 A fast sequential Markov coalescent simulation of genomic data under complex evolutionary models

msprime Another fast sequential Markov coalescent simulation of genomic data under complex evolutionary models
Spatial Coalescence

SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios

IBDSim is a package for the simulation of genotypic data under isolation by distance. It is based on a backward ‘generation by generation’ coalescent algorithm allowing the consideration of various isolation by distance models with discrete subpopulations as well as continuous populations

CDPOP is a spatiallyexplicit simulator of geneflow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics

BayeSSC (Bayesian Serial SimCoal) is a Bayesian modification of SIMCOAL 1

KERNELPOP This package creates a individualbased population genetic simulation. Individuals have spatial coordinates, dispersal governed by mixtures of Weibull and normal pdfs

BOTTLESIM is a computer simulation program for simulating the process of population bottlenecks

MS for generating samples/coalescent trees under a WrightFisher neutral model

ALADYN a spatially explicit, allelic model for simulating adaptive dynamics (LINK2) ALADYN facilitates the investigation of adaptive processes to spatially and/or temporally changing conditions and the resulting niche and range dynamics. Allows a continuous resolution of individuals' locations in a spatially explicit landscape together with the associated patterns of selection

GINKGO a software package for agentbased, forwardtime simulations of genealogies of multiple unlinked loci from diploid populations
Other Evolutionary Genetics Software
Swiss Army Knives

Geneious. A powerful and comprehensive suite of molecular biology and NGS analysis tools. Great, but expensive

Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms
Alignments

Clustal is the classic multiple sequence alignment program

Muscle is a newer multiple sequence alignment program

MAFT is the newest multiple sequence alignment program
Phasing Alleles

Phase a software for haplotype reconstruction, and recombination rate estimation from population data
PhylogeneticsLikelihood

Raxml is a popular program for phylogenetic analysis of large datasets under maximumlikelihood

PhyML an alternative algorithm to RAxML

ExaML for huge analyses

Garli is a classic program for phylogenetic analysis
PhylogeneticsBayesian

MrBayes is the classic and very versatile Bayesian inference system geared towards phylogenetic analysis.

RevBayes is a very versatile Bayesian inference system geared towards phylogenetic analysis. It has an Rlike interface with its own language Rev. Theory Tutorial Example Report

Sate program Sate estimates a phylogenetic tree and aligns sequences at the same time. Theory Tutorial Example Report

ExaBayes for huge Bayesian analysis
Species Tree & Chronograms

BEAST 1.8 Skyline is a versatile package to analyze phylogenies population expansion and plots of parameters through time. Theory Tutorial Example Report

BEAST 2.3 SNAPP allows to estimate a species tree from unlinked single nucleotide polymorphims (SNP). Theory Tutorial Example Report

ASTRAL Uses the quartet supertree method to reconstruct phylogenies with large numbers of loci
Tree Visualization

DensiTree is a program for qualitative analysis of sets of trees

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publicationready figures
Haplotype Networks

SPADS (for “Spatial and Population Analysis of DNA Sequences”) is a population genetics toolbox computing several summary statistics from populations or groups of populations, performing several input file conversions for other population genetics programs and implementing two clustering algorithms to study the genetic structure of populations
Migration and Population Sizes (nonABC methods)

LaMARC is a program which estimates populationgenetic parameters such as population size, population growth rate, recombination rate, and migration rates

IM/IMa2 IM is a program for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. Theory Tutorial Example Report

Migraten estimates population sizes, migration rates, and (in a very recent version) divergence times and among populations using sequence or microsatellite data. Theory Tutorial MBLTutorial Example Report
Genetic Distances

MEGA Sophisticated and userfriendly software suite for analyzing DNA and protein sequence data from species and populations
Standard Population Genetic Summary Statistics

Genepop: Genepop on the Web and Genepop Software This software calculates standard population genetic quantities, such as FST, isolation by distance measures etc. Theory; Tutorial material: download GENEPOP_TUTORIAL.ZIP

Arlequin The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples

Geneland The program Geneland (it is an R package an can be installed from any CRAN site  see instructions) Theory Tutorial Example Report
Population Delimitation

Structure is a free software package for using multilocus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Theory Tutorial Example Report

StructurRama is a program for inferring population structure from genetic data. The program assumes that the sampled loci are in linkage equilibrium and that the allele frequencies for each population are drawn from a Dirichlet probability distribution

Treemix a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modernday populations in a species are related to a common ancestor via a graph of ancestral populations. Theory Tutorial

ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm

SNMF uses sparse nonnegative matrix factorization to estimate admixture coefficient, and performs as well as ADMIXTURE, but much faster
Approximate Bayesian Computation (ABC)

ABCtoolbox was designed to perform ABC estimations using various recently published algorithms including MCMC without likelihood and Population Monte Carlo. Due to its potential to interact with almost any command line simulation software, ABCtoolbox can be used to study problems in different areas including genomics or population genetics

MSbayes can test for simultaneous divergence or colonization across multiple codistributed pairs of taxa (populations and/or species). It uses hierarchical approximate Bayesian computation (HABC) to estimate hyperparameters given DNA sequence data

DIYABC a userfriendly approach to Approximate Bayesian Computation for inference on population history using molecular markers
Site Frequency Spectrum

Dadi uses the site frequency spectrum to evaluate complex population models, up to three populations. Theory Tutorial Example Report

MultiDICE (Multiple Taxa Demographic Inference of Congruency in Events)  R package for constructing hierarchical codemographic models and simulating multitaxa summary statistic vectors