miniMDS |
Optimization |
Success |
Yes |
BACH |
Modeling |
Bug |
No |
ShRec3D |
Optimization |
Success |
No |
MOGEN (Trieu and Cheng, 2014) |
Optimization |
Exceeds maximum input size |
No |
3D-GNOME (Szałaj et al., 2016) |
Optimization |
Success (graphical output only) |
Yes |
ChromSDE (Zhang et al., 2013) |
Optimization |
Failed to produce output in reasonable time |
No |
tRex (Park and Lin, 2016) |
Modeling |
Requires fragment length |
No |
MCMC5 (Rousseau et al., 2011) |
Modeling |
Requires standard deviation |
No |
PASTIS (Varoquaux et al., 2014) |
Modeling |
Failed to install IPOPT |
Yes |
TAD-bit (Baù and Marti-Renom, 2012) |
Optimization |
Failed to produce output in reasonable time |
Yes |
HSA (Zou et al., 2016) |
Modeling |
Memory error |
No |
Chromosome3D (Adhikari et al., 2016) |
Optimization |
Failed to produce output in reasonable time |
No |
InfMod3DGen (Wang et al., 2015) |
Modeling |
Bug (error was corrected while the current manuscript was in press) |
No |