Table 1.
Evaluated Software Packages per Application Domain Including Version Numbers.
| Domain | Software | Version Number |
|---|---|---|
| Phylogenetics | PAML (Yang 2007) | 4.8 |
| PHYML (Guindon et al. 2010) | 20141009 | |
| MrBayes (Ronquist et al. 2012) | 3.2.4-svn(r926) | |
| RAxML (Stamatakis 2014) | 8.2.11 | |
| Population genetics | MS (Hudson 2002) | Sep 8, 2014 |
| SweepFinder (Nielsen et al. 2005) | Feb 23, 2015 | |
| Seq. alignment | MAFFT (Katoh and Standley 2013) | 7.205 |
| T-Coffee (Notredame et al. 2000) | 20141026_23: 18 | |
| Prank (Löytynoja and Goldman 2005) | 140603 | |
| Div. times | Beast (Drummond and Rambaut 2007) | 1.8.0 |
| FDPPDIV (Heath et al. 2014) | 1.3 | |
| Multi.-Sp. coalescence | BP&P (Yang and Rannala 2010) | 3.0 |
| Seq. simulation | Seq-Gen (Rambaut and Grass 1997) | 1.3.3 |
| INDELible (Fletcher and Yang 2009) | 1.0.3 | |
| De novo assembly | SOAP (Li et al. 2009) | r240 |
| Abyss (Simpson et al. 2009) | 1.5.2 | |
| Astrophysics | Gadget-2 (Springel 2005) | 2.0.7 |
Note.—As MS and SweepFinder do not have version numbers we show the download dates.