Table 1

CPU time and memory requirements for SiLiX and three state-of-the-art programs on the dataset of similarity pairs extracted from the HOGENOM database [9].

method

CPU (min)

RAM (GB)


SiLiX

138

0.4

SiLiX + hcluster_sg(100) [24]

552

23

hcluster_sg [24]

5604

99

MC-UPGMA [25]

>27000(1)

0.5

MCL [26]

>15000(2)

78

(1) estimated time (20 rounds took 2711 min., and 200 rounds were required in [25])

(2) manually stopped


hcluster_sg(100) corresponds to the use of hcluster_sg on the largest families (more than 100 sequences) retrieved by SiLiX with permissive similarity thresholds (sequence identity 25% and alignment coverage 80%). SiLiX and MC-UPGMA run on a quadri-quadcore Xeon 2.66 GHz with 24 GB RAM, hcluster_sg and MCL on a octo-quadcore Opteron 2.3 GHz with 64 GB RAM.

Miele et al. BMC Bioinformatics 2011 12:116   doi:10.1186/1471-2105-12-116

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