The main software used to simulate genetic sequences under nucleotide, codon, and amino acid substitution models.

“Class” includes phylogenetic (where a genealogy is already given from the user), forward, birth-death, and coalescent approaches. “Process” shows the implemented evolutionary scenarios: “D”, “Pm”, “R”, and “S” indicate demographics, population structure and migration, recombination, and selection, respectively. “Substitution model” refers to substitution models based on nucleotide “Nt”, codon “Cod”, and amino acid “Aa” sequences; indeed, “Nt: All” indicates all nucleotide substitution models developed so far (JC, …, GTR) and “EM” indicates empirical model. “Rate variation” indicates whether different sites can be evolved under different rates (G: gamma distribution; I: proportion of invariable sites). “Indels” indicates the consideration of insertion and deletion events. “OS” shows the availability of executable files and/or source code “SC” for different operative systems (“All” means that Macintosh, Windows, and Linux executables are available), and “R” means the R language for statistical computing. “Ref” indicates the reference of publication. Although many more software packages exist, here I have selected, from my point of view, those programs most commonly used, most user-friendly, and which implement the most diverse range of evolutionary scenarios.aIntracodon recombination is also allowed in NetRecodon and GenomePop.bThe ARG can be exported from NetRecodon and can be then visualized and analyzed using NetTest[78].cUnder codon models, ω can change across codons.dCoding sequences are simulated by nucleotide substitution models, avoiding stop codons.eEvolSimulator simulates phylogenetic histories under the birth-death model of speciation and extinction [79].fUnder codon models, ω can change across codons and branches.gAmino acid models implemented in INDELible: BLOSUM62, CpREV, DAYHOFF, DAYHOFF (DCMUT), HIVb, HIVw, JTT, JTT (DCMUT), LG, mtArt, MTMAM, mtREV, RtREV, VT, and WAG.hAmino acid models implemented in EVOLVER: CpREV, CpREV64, DAYHOFF (DCMUT), DAYHOFF, GRANTHAM, JTT (DCMUT), JTT, LG, miyata, mtArt, MTMAM, mtREV24, mtZoa, WAG.iAmino acid models implemented in Seq-Gen: BLOSUM62, CpREV24, JTT, mtREV, PAM, and WAG.jSimulation of codons with structural dependency among sites.kThe rate of variation among sites can be introduced from the user.lAmino acid models implemented in ALF: PAM, JTT, WAG, LG, CustomP, GCB.mAmino acid models implemented in PhyloSim: CpREV, JTT, JTT (DCMUT), LG, mtArt, mtMam, mtREV24, mtZoa, WAG.