WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

Table 1 Statistics of the WGDdetector performance on the test data

Software	Date type	Clean genes	Number of threads^a	Elapsed time (hour)^b	Max memory used (Gb)	Number ofsub-gene families^c
ADHoRe	A. thaliana (genome)	27,301	15; 1	1.79 (1.05 + 0.74)	0.94	6649
	J. regia (genome)	32,436	15; 1	2.09 (1.23 + 0.86)	2.11	6127
	P. trichocarpa (genome)	39,410	15; 1	4.18 (1.51 + 2.67)	2.52	22,676
	X. laevis (genome)	41,073	15; 1	4.82 (2.24 + 2.58)	4.08	14,055
MCScanX	A. thaliana (genome)	27,301	15; 1	1.62 (1.05 + 0.57)	0.73	14,363
	J. regia (genome)	32,436	15; 1	2.64 (1.23 + 1.41)	1.44	4333
	P. trichocarpa (genome)	39,410	15; 1	2.21 (1.51 + 0.70)	1.56	21,643
	X. laevis (genome)	41,073	15; 1	6.27 (2.24 + 4.03)	1.65	23,721
WGDdetector	A. thaliana (genome)	27,301	15	5.57	9.16	6729
	A. thaliana (RNA-seq)	23,495	15	6.32	6.32	6072
	J. regia (genome)	32,436	15	8.88	15.56	8504
	P. trichocarpa (genome)	39,410	15	11.65	11.65	9818
	P. trichocarpa (RNA-seq)	20,354	15	5.18	11.84	5191
	X. laevis (genome)	41,073	15	19.23	35.46	9391

^aThe format of “15; 1” representing the number of threads when protein clustering and the dS calculating
^bThe format “S (X + Y)” represent the total elapsed time (S), the protein clustering elapsed time (X) and the dS calculating elapsed time (Y)
^cIn the software ADHoRe and MCScanX, all the homologous genes were recorded. In the WGDdetector pipeline, only the sub-gene families were recoded

ISSN: 1471-2105