Skip to main content

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].

From: Ultra-fast sequence clustering from similarity networks with SiLiX

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
 
  1. 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.