Table 1 Comparison of time complexity of OrthoMCL, GCFinder and SYNS All experiments have been run on the dual-core Intel Xeon 2.33 GHz server. Results are also available for MultiParanoid (approx. 2 hours run time) and CoCo-CL (approx 3 hours run time) for which no time complexity is found in literature.
From: Identification of conserved gene clusters in multiple genomes based on synteny and homology
Method | Time complexity | Execution time | Notations Used |
|---|---|---|---|
OrthoMCL | O(Nk2) | 76min (excluding Blast) | N = #genes, k = pruning constant |
GCFinder Ordered Unordered | O(nd(k + d)) O(k2nD(tD + 1)k- 1) | 1546min interrupted after 3 days | n = #families k = #genes, d = window size D = max #genes in a window t = max # paralogous copies of a gene in a chr. |
SYNS | O(n((δ + 1) × c × t)4) | 15min | n = #families, c = #chr., δ = window size, t = max # of paralogous copies of a gene in a chr. |