Table 1.
Substitution models implemented in relevant software for phylogenetic inference.
| Program | Task | Substitution model | Genome | Rate variation | References | ||
|---|---|---|---|---|---|---|---|
| Non-coding | Coding | Amino acid | |||||
| PhyML | Inference | All | – | Blosum62, CpRev, Dayhoff, FLU, HIVb, HIVw, JTT, LG, Mtart, Mtmam, Mtrev, RtRev, VT, WAG +F | – | +I +G | Guindon et al., 2010 |
| CodonPhyML | Inference | – | GY94b, MG94, YAP, ECMs | – | – | +G | Gil et al., 2013 |
| RAxML | Inference | JC, K80, HKY, GTR | Nta | Blosum62, CpRev, Dayhoff, DUMMY, FLU, HIVb, HIVw, JTT, JonesDCMUT, LG, Mtart, Mtmam, Mtrev, Mtzoa, PMB, RtRev, STMREV, VT, WAG +F | Partitioned models can be specified | +I +G | Stamatakis, 2006 |
| MEGA | Inference | JC, K2P, HKY, TN93, GTR | NG86 | CpRev, Dayhoff, JTT, LG, MtRev, RtRev, WAG | – | +I +G | Tamura et al., 2013 |
| Hyphy | Inference | All | GY94b, MG94, ECM | Dayhoff, HIVb, HIVw, JTT, Mtmam, Mtrev, RtRev, WAG +F | Partitioned models can be specified | +I +G | Pond et al., 2005 |
| PAML | Inference | All | GY94b, c, ECMs | CpRev, Dayhoff, DayhoffDCMUT, Grantham, JTT, JonesDCMUT, LG, Miyata, Mtart, Mtmam, Mtrev24, Mtzoa, WAG +F | – | +I +G | Yang, 2007 |
| MrBayes and BEST | Inference | All | GY94b, MG94 | Blosum62, CpRev, Dayhoff, Mtmam, Mtrev, RtRev, VT, WAG +F | Partitioned models can be specified | +I +G | Ronquist et al., 2012 |
| BEAST | Inference | JC, HKY, TN93, GTR | Nta | Blosum62, CpRev, Dayhoff, FLU, JTT, LG, Mtrev, WAG | – | +I +G | Bouckaert et al., 2014 |
| OmegaMap | Inference | – | NY98b | – | – | – | Wilson and McVean, 2006 |
| Lamarc | Inference | JC, K2P, F84, GTR | – | – | – | +G | Kuhner, 2006 |
| CodABC | Inference | – | GY94 | – | – | +I +G | Arenas et al., 2015a |
| MySSP | Simulation | All | – | – | – | +G | Rosenberg, 2005 |
| Seq-Gen | Simulation | All | Nta | Blosum62, CpRev, JTT, mtREV, PAM, and WAG +F | – | +I +G | Rambaut and Grassly, 1997 |
| indel-Seq-Gen | Simulation | All | Nta | Blosum62, CpRev, JTT, mtREV, PAM, WAG +F | – | +I +G | Strope et al., 2009 |
| INDELible | Simulation | All | GY94b, c, ECMs | Blosum62, CpRev, Dayhoff, DayhoffDCMUT, HIVb, HIVw, JTT, JonesDCMUT, LG, Mtart, Mtmam, Mtrev24, RtRev, VT, WAG +F | – | +I +G | Fletcher and Yang, 2009 |
| EVOLVER | Simulation | All | GY94b, c, ECMs | CpRev, Dayhoff, DayhoffDCMUT, Grantham, JTT, JonesDCMUT, LG, Miyata, Mtart, Mtmam, Mtrev24, Mtzoa, WAG +F | – | +I +G | Yang, 2007 |
| Recodon and NetRecodon | Simulation | All | GY94b | – | – | +I +G | Arenas and Posada, 2007, 2010 |
| ProteinEvolver | Simulation | All | – | 3D structural constraints, Blosum62, CpRev, Dayhoff, DayhoffDCMUT, HIVb, HIVw, JTT, JonesDCMUT, LG, Mtart, Mtmam, Mtrev24, RtRev, VT, WAG +F | – | +I +G | Arenas et al., 2013 |
| CoalEvol | Simulation | All | GY94b, c, MG94, ECMs, HB | Blosum62, CpRev, Dayhoff, DayhoffDCMUT, HIVb, HIVw, JTT, JonesDCMUT, LG, Mtart, Mtmam, Mtrev24, RtRev, VT, WAG +F | – | +I +G | Arenas and Posada, 2014b |
| SIMPROT | Simulation | – | – | PAM, JTT, PMB | – | +G | Pang et al., 2005 |
| PhyloSim | Simulation | All | GY94b, c, ECMs | CpRev, JTT, JonesDCMUT, LG, Mtart, Mtmam, Mtrev24, Mtzoa, WAG +F | – | +I +G | Sipos et al., 2011 |
| π BUSS | Simulation | HKY, TN93, GTR | GY94, MG94 | BLOSUM, Dayhoff, LG, JTT, WAG +F | – | +I +G | Bielejec et al., 2014 |
| SGWE | Simulation | All | GY94b, c, MG94, ECMs, HB | Blosum62, CpRev, Dayhoff, DayhoffDCMUT, HIVb, HIVw, JTT, JonesDCMUT, LG, Mtart, Mtmam, Mtrev24, RtRev, VT, WAG +F | User-specified regions | +I +G | Arenas and Posada, 2014b |
| ALF | Simulation | F84, HKY, TN93, GTR | GY94b, ECMs | Gonnet, JTT, LG, PAM, WAG +F | User-specified regions | +I +G | Dalquen et al., 2012 |
“Task” indicates if the program is oriented to perform evolutionary inference or simulation of molecular evolution. “Substitution model” indicates the implemented models of non-coding DNA evolution [“All” means that all the reversible nucleotide substitution models are considered, JC, …, GTR], codon models [“ECMs” indicates empirical codon models, MG94 model refers to Muse and Gaut (1994) and HB model refers to Halpern and Bruno (1998)] and amino acid models [“+F” indicates that amino acid frequencies can be modeled]. “Rate variation” includes proportion of invariable sites “+I” and substitution rate heterogeneity across sites according to a gamma distribution “+G.” “Genome” indicates the consideration of genome evolution through region-specific substitution models.
Coding sequences are simulated by nucleotide substitution models, avoiding stop codons.
dN/dS can vary across codons.
dN/dS can vary across branches.