Table 1. Method run-times on the Arabidopsis Array-CGH data set.

Shortcut	Method	Reference	Computing time
wuHMM	First-order HMM	[56]	8 min
GHMM	Bayesian first-order HMM	[52]	24 min
PHMM	Parsimonious fourth-order HMM	see Methods	54 min
CBS	Circular Binary Segmentation	[20]	1 h 18 min
ACE	Analysis of Copy Errors	[33]	4 h 14 min
GLAD	Gain and Loss Analysis of DNA	[32]	4 h 19 min
FHMM	First-order HMM	[48]	5 h 04 min
RJaCGH	Bayesian first-order HMM	[55]	30 h 42 min

Run-times in hours/minutes required for the analysis of the Arabidopsis Array-CGH data set by the different methods. All methods except GHMM, PHMM, wuHMM, and RJaCGH were run on the ADaCGH web-server [43] (AMD Opteron 2.2 GHz CPU with 6 GB RAM). The other methods GHMM, PHMM, wuHMM, and RJaCGH were run on a standard desktop computer with Intel CPU T9500 2.6 GHz and 4 GB RAM.