Benchmarks

Time (seconds) / RAM (Mb) benchmarks for TriFusion

These benchmarks were clocked with the CLI version of TriFsion for the Process module (TriSeq). The GUI version can be a bit slower.

Hardware: Intel i7-7500 @ 2.70Ghz - HD620 - NVMe SSD

	DS1	DS2	DS3	DS4	DS5	DS6	DS7	DS8	DS9	DS10
Files	614	3093	3093	3093	7378	1	1	1	1	2
Taxa	48	48	141	376	29	40	40	40	376	40
Total bases / taxon	~350k	1.25M	1.25M	1.25M	~601k	4.5M	4.5M	4.5M	1.25M	9M
Notes							Interleave (phylip)	Interleave (nexus)
Parsing
Alignment reading	0.8 / 13.9	4.6 / 53.8	7.8 / 86.2	14.5 / 169.5	13.6 / 117.6	1.2 / 33.5	2.7 / 27.2	69.8 / 23.6	2.9 / 14.5	2.4 / 42.1
Main operations
Conversion (nexus)	0.5 / 0.3	10.4 / 0.6	12.2 / 0.4	17.0 / 0.6	93.7 / 1.0	1.0 / 69.2	1.0 / 65.1	1.0 / 73.5	2.4 / 22.8	1.5 / 69.5
Conversion (interleave)	2.4 / 0.4	18.1 / 0.6	27.7 / 0.5	49.9 / 0.6	110.1 / 1.0	19.1 / 51.9	18.9 / 56.2	18.8 / 56.2	74.9 / 17.0	36.8 / 52.0
Concatenation	4.7 / 5.1	60.1 / 20.7	196.6 / 21.8	554.4 / 21.6	211.2 / 7.1	NA	NA	NA	NA	1.7 / 34.8
Secondary operations
Collapse	0.9 / 0.3	9.1 / 0.2	11.8 / 0.5	15.1 / 0.4	56.1 / 0.1	1.3 / 61.2	1.3 / 65.7	1.3 / 66.3	3.2 / 21.1	2.8 / 61.5
Consensus (Soft mask/ single file)	2.3 /** 2.4**	13.1 / 9.2	17.4 / 8.5	27.8 / 4.7	24.7 / 9.3	19.1 / 58.3	18.6 / 56.1	19.8 / 53.5	34.2 / 151.0	37.6 / 75.7
Filter (Taxa contain)	0.8 / 2.1	45.9 / 4.8	65.6 / 4.9	104.9 / 4.9	18.8 / 9.2	NA	NA	NA	NA	0.0 / 0.3
Filter (Missing data; G50; M75)	7.0 / 0.8	43.0 / 0.9	70.5 / 1.6	159.4 / 3.4	149.8 / 1.7	54.8 / 144.6	55.9 / 152.9	59.6 / 154.9	163.8 / 155.6	112.0 / 148.6
Filter (Codons; 1 2)	3.3 / 0.5	16.8 / 0.6	30.2 / 0.4	60.1 / 0.6	65.7 / 1.6	17.6 / 150.3	17.3 / 153.6	18.4 / 152.9	60.2 / 38.0	35.5 / 144.9
Filter (Variable; 0, 200)	2.0 / 2.2	55.3 / 5.2	75.8 / 5.4	128.9 / 6.5	10.7 / 0.9	NA	NA	NA	NA	0.1 / 11.4
Filter (Informative; 0, 200)	7.1 / 2.4	78.5 / 5.0	121.8 / 5.6	235.7 / 7.9	22.9 / 1.0	NA	NA	NA	NA	0.7 / 6.4
Reverse concatenation +
Conversion (nexus)	4.4 / 8.3	58.3 / 40.1	158.9 / 75.8	407.9 / 120.2	170.7 / 95.3	NA	NA	NA	NA	4.4 / 155.1