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

<p>“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.</p>a<p>Intracodon recombination is also allowed in <i>NetRecodon</i> and <i>GenomePop</i>.</p>b<p>The ARG can be exported from <i>NetRecodon</i> and can be then visualized and analyzed using <i>NetTest</i><a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002495#pcbi.1002495-Arenas9" target="_blank">[78]</a>.</p>c<p>Under codon models, <i>ω</i> can change across codons.</p>d<p>Coding sequences are simulated by nucleotide substitution models, avoiding stop codons.</p>e<p>EvolSimulator simulates phylogenetic histories under the birth-death model of speciation and extinction <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002495#pcbi.1002495-Raup1" target="_blank">[79]</a>.</p>f<p>Under codon models, <i>ω</i> can change across codons and branches.</p>g<p>Amino acid models implemented in <i>INDELible</i>: BLOSUM62, CpREV, DAYHOFF, DAYHOFF (DCMUT), HIVb, HIVw, JTT, JTT (DCMUT), LG, mtArt, MTMAM, mtREV, RtREV, VT, and WAG.</p>h<p>Amino acid models implemented in <i>EVOLVER</i>: CpREV, CpREV64, DAYHOFF (DCMUT), DAYHOFF, GRANTHAM, JTT (DCMUT), JTT, LG, miyata, mtArt, MTMAM, mtREV24, mtZoa, WAG.</p>i<p>Amino acid models implemented in <i>Seq-Gen</i>: BLOSUM62, CpREV24, JTT, mtREV, PAM, and WAG.</p>j<p>Simulation of codons with structural dependency among sites.</p>k<p>The rate of variation among sites can be introduced from the user.</p>l<p>Amino acid models implemented in <i>ALF</i>: PAM, JTT, WAG, LG, CustomP, GCB.</p>m<p>Amino acid models implemented in <i>PhyloSim</i>: CpREV, JTT, JTT (DCMUT), LG, mtArt, mtMam, mtREV24, mtZoa, WAG.