Table 1

Algorithms available to run in Auto-SAM

Algorithm

Type

Input

Output

Mouse run Time (traits)

Mouse run time (genes)

Yeast run time

Automated steps


GFlasso [13]

SAM

G, P, Ep

G-P association

0 05:05:50

1 16:17:45

2 06:43:56

17


MPGL [11]

SAM

G, P, Pop

G-P association

2 09:07:47

-

3 11:09:46

3


TreeLasso [10]

SAM

G, P, Ep

G-P association

0 01:12:03

0 12:53:52

0 05:08:42

15


AMTL [12]

SAM

G, P, Fg

G-P association

-

-

1 20:35:47

8


gGFlasso [14]

SAM

T, Et, P, Ep, G/T assoc

T-P association

N/A

0 01:54:04

N/A

19


Wald Test [15]

AM

G, P

G-P association

0 00:23:29

0 09:51:23

0 00:54:04

5


Wilcoxon Sum-rank test [8]

AM

G, P

G-P association

0 00:10:21

0 01:05:51

0 00:14:32

4


Lasso [16]

AM

G, P

G-P association

0 00:59:21

0 08:22:42

0 04:07:53

6


association by population [17]

AM

G, P, Pop

G-P association

0 00:57:24

2 19:02:46

1 03:00:44

5


Correlation

network

P

Ep

0 00:01:50

0 00:06:05

0 00:09:29

3


Glasso [18]

network

P

Ep

0 00:07:31

0 01:19:37

0 01:51:24

10


Scale-free network [19]

network

P

Ep

0 00:03:11

0 00:41:23

0 00:41:08

6


Hierarchical clustering

tree

P

tree

0 00:43:32

0 01:27:32

0 01:05:04

3


Structure [20]

population

G

Pop

0 13:30:32

0 13:30:32

0 00:41:54

4


Gene module discovery [8]

Network analysis

Ep

phenotype clusters

N/A

0 12:29:24

0 01:03:22

4


We present a list of all algorithms available to run through the Auto-SAM system and GenAMap. We group the algorithms by type: SAM (structured association mapping), AM (association mapping), network generation, tree generation, population determination, and network analysis. The input for each algorithm can be G (genotype), P (phenotype), T (gene expression data), Ep (edges for the phenotype), Fg (features of the genotype), Et (edges for the gene expression values), and G/T (genome/transcriptome) associations. Times are represented as D HH:MM:SS where D day, H hour, M minute, and S second.

Curtis et al. BMC Genetics 2012 13:24   doi:10.1186/1471-2156-13-24

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