| | Evolutionary modelling | Implementation |
|---|
Program | Codons1 | Amino acids2 | Indels | Partitions | Molecular clocks | Ancestral sequences | Coalescent models3 | GUI | Multi-core | Cross-platform4 |
|---|
πBUSS | X | X | | X | X | X | X | X | X | X |
Seq-Gen [7] | | X | | X | | | | | | X |
indel-Seq-Gen2 [32] | | X | X | X | | X | | | | X |
PhyloSim [33] | X | X | X | X | | X | | | | X |
Recodon [34] | X | | | | | X | X | | X | X |
NetRecodon [35] | X | | | | | X | X | | X | X |
Indelible [36] | X | X | X | X | | | | X | | |
DAWG [37] | | | X | | | X | X | | | X |
Mesquite [38] | | | | | | X | X | X | | X |
Rose [39] | | | X | | | X | | | | |
Evolver [8] | X | X | | X | | X | | | | X |
ProteinEvolver [40] | | X | | | | X | X | | X | X |
ALF [41] | X | X | X | X | | X | X | X | | X |
GenomePop [42] | X | | | | | X | X5 | | | X |
SIMCOAL [43] | | | | | | X | X | | | X |
SIMPROT [44] | | X | X | | | X | | X | | X |
- 1πBUSS: GY94, MG94; PhyloSim: GY94 x M0 - M4; Recodon: GY94 x M0, M1, M7, M8; NetRecodon: GY94 x M0, M1, M7, M8; Indelible: GY94 x M0 - M10; Evolver: GY94 x M0, M1, M2, M3, M7, M8; ALF: GY94 x M0, M1, M7 and M8; GenomePop: MG94. 2πBUSS: BLOSUM [25], CPREV [45], Dayhoff [23], FLU [46], JTT [24], LG [27], MTREV [47], WAG [26]; Seq-Gen: JTT, WAG, PAM [48], BLOSUM, MTREV; indel-Seq-Gen2: PAM, JTT, MTREV, CPREV; PhyloSim: CPREV, JTT, LG, MTART [49], MTMAM [50], MTREV24 [51], MTZOA [52], PAM, WAG; Indelible: Dayhoff, JTT, WAG, VT [53], LG, BLOSUM, MTMAM, MTREV, MTART, CPREV, RTREV [54], HIVb [55], HIVw [55]; Evolver: Dayhoff, JTT, WAG, MTMAM, MTREV; ProteinEvolver: BLOSUM, CPREV, Dayhoff, HIVb, HIVw, JTT, Jones [24], LG, MTART, MTMAM, MTREV24, RTREV, VT, WAG; ALF: PAM,GTT,LG,WAG; SIMPROT: PAM, JTT, PMB. 3πBUSS: demography; Recodon: recombination, migration, demography; NetRecodon: recombination, migration, demography; Mesquite: speciation; ProteinEvolver: recombination, migration, demography; SIMCOAL: demography and migration. 4PhyloSim: R package; Indelible: Executables for Windows and MacOS; ALF: Web interface; GenomePop: Executables for Windows and Linux; SIMCOAL: Executables for Windows; SIMPROT: GUI, Web interface; SIMPROT: Executables for Windows and Linux. 5Forward simulation including recombination, demography and migration.
