AF | Tools

Alignment-free tools

Tools Parameters

Benchmarked Tools

Overview of parameter ranges of alignment-free sequence comparison tools tested across 12 reference data sets.

Tool	Method	Tool Version	Regulatory Sequences	Protein Sequence Classification	Gene Tree Inference	Genome-based Phylogeny					Horizonal Gene Transfer
						Full genome sequences			Unassembled reads		E.coli / Shigella	Yersinia	Simulated genomes
						fish mtDNA	E.coli	Plants	E.coli	Plants	E.coli / Shigella	Yersinia	Simulated genomes
AAF		10/01/2017							k ϵ [6-29] corrected/uncorrected tip branches
AFKS	afd canberra chi_squared d2s d2_star d2z emd euclidean euclidean_z harmonic_mean hellinger jaccard jefferey_divergence jensen_shannon k_divergence kl_conditional kulczynski1 kulczynski2 length_difference manhattan markov mismatch n2r n2rc n2rrc normalized_vectors pearson rre_k_r sim_mm simratio spearman squared_chord	1.0	k ϵ [2-6]	k ϵ [1-3]	k ϵ [1-3]	k ϵ [5-8]	k ϵ [9-12]	k ϵ [12-13]	k ϵ [6-9]	k ϵ [7-8]	k ϵ [9-13]	k ϵ [9-13]	k ϵ [8-12]
alfpy	angle_cos_diss angle_cos_evol braycurtis canberra chebyshev google W-metric	1.0.6	k ϵ [2-7] counts,freqs	k ϵ [1-5] counts, freqs Wmetric: BLOSUM30-95	k ϵ [1-10] counts, freqs	k ϵ [4-29] counts, freqs	k ϵ [6-29] counts, freqs	k ϵ [6-13] counts, freqs			k ϵ [8-29] counts, freqs	k ϵ [8-20] counts, freqs	k ϵ [8-29] counts, freqs
ALFRED-G		NA	default (k=1; x=0) k ϵ [0-3] & x ϵ [1-10]	default (k=1; x=0) k ϵ [0-1] & x ϵ [1-5]		default (k=1; x=0) k ϵ [1-2] & x ϵ [1-29]	default (k=1; x=0) k=1 & x ϵ [1-5]				default (k=1; x=0) k=1 & x ϵ [1-10]		default (k=1; x=0) k ϵ [0-1] & x ϵ [1-7]
andi		0.02				p ϵ [0.0001, 0.0005, 0.001, 0.005, 0.01, 0.025, 0.05, 0.075, 0.1, 0.15] m ϵ [JC, Kimura]					p ϵ [0.0001, 0.0005, 0.001, 0.005, 0.01, 0.025, 0.05, 0.075, 0.1, 0.15] m ϵ [JC, Kimura]
CAFE	cafe-cvtree cafe-d2shepp cafe-d2star	1.0.0	k ϵ [4-6] M ϵ [0-2]			k ϵ [3-10] M ϵ [0-1]	k ϵ [12-13] M ϵ [0-1]	k ϵ [9-11] M ϵ [7-9]	k ϵ [12-13] M ϵ [0-1]	k ϵ [9-11] M ϵ [7-9]	k ϵ [7,2,13] M ϵ [0-5]	k ϵ [6,2,13] M ϵ [0,4]	k ϵ [12-13] M ϵ [0-2]
co-phylog		NA				default, HALFCTX ϵ [5-8]	default	default, HALFCTX ϵ [11-12]	default	default, HALFCTX ϵ [11-12]	default	default	default
EP-sim		1.0	L ϵ [3-8] P ϵ [07, 085] D ϵ [D2, D2S]	L ϵ [2-7] P = 07 D ϵ [D2, D2S]	L ϵ [3-7] P = 07 D ϵ [D2, D2S]	L ϵ [3-7] P = 07 D ϵ [D2, D2S]	L ϵ [3-7] P = 07 D ϵ [D2, D2S]	L ϵ [3-5] P = 07 D ϵ [D2, D2S]			L ϵ [3-7] P = 07 D ϵ [D2, D2S]	L ϵ [3-7] P = 07 D ϵ [D2, D2S]	-
FFP		2.2017	k ϵ [2-7]	k ϵ [2-6]	k ϵ [4-15]	k ϵ [4-29]	k ϵ [10-29]	k ϵ [8-15]	k ϵ [9-17]		k ϵ [10-29]		k ϵ [10-24]
FSWM/Read-SpaM		1.0				pat. length ϵ [8,10,12] pat. weight = 12	default	default	pat. length ϵ [72, 82] pat. weight = 12	pat. length = 72	default	default	default
jD2Stat	d2n D2S D2St	1.0	k ϵ [4-10]		k ϵ [3-10]	D2n: k ϵ [4-10] D2S: k ϵ [4-26] D2St: k ϵ [4-10]	k ϵ [5-26]				k ϵ [5-26]
kmacs		1.0	default	default		k ϵ [5,10,15,20]	default				default	default	default
kr		2.0.2	default			default	default				default	default	default
kSNP3.0		3.1				k ϵ [9-29]	k ϵ [9-15]	k ϵ [9-12]			k ϵ [10-13]	k ϵ [11-18]	k ϵ [9-12]
kWIP		0.2.0-13-g3cf8a9e							k ϵ [9-27]
LZW-Kernel	LZW-Kernel LZW-NCD	NA	default	default	default	default	default	default			default	default	default
mash		2.1	k ϵ [2-7] s ϵ [1k, 5k, 10M]	k ϵ [2-5] s ϵ [1k, 5k, 10k, 10M]	k ϵ [2-15] s ϵ [1k, 5k, 10k, 15k, 20k, 10M]	k ϵ [11-32] s ϵ [1k, 5k, 10k, 15k, 20k]	k ϵ [11-29] s ϵ [1k, 5k, 10k, 15k, 20k, 25k, 30k, 35k, 40k, 50k, 100k, 1M, 10M]	k ϵ [11-29] s ϵ [1k, 5k, 10k, 15k, 20k, 25k, 30k, 35k]	k ϵ [6-32] s ϵ [1k, 5k, 10k, 15k, 20k, 25k, 30k, 35k, 40k, 50k, 100k, 1M, 10M] -r ϵ [True, False]		k ϵ [11-32] s ϵ [1k, 5k, 10k, 15k, 20k, 25k, 30k, 35k, 40k, 50k, 100k, 500k, 1M, 10M]
Multi-SpaM		1.0				default	default	default			default	default	default
Phylonium		0.3				default	default	default			default	default
RTD-Phylogeny		1.0.1	k ϵ [1-7]	k ϵ [1-3]	k ϵ [1-4]	k ϵ [1-7]					k ϵ [1-7]
Skmer		3.0.0				k ϵ [21-31] -t (JC model)			k ϵ [21-31] -t (JC model)	k ϵ [21-31] -t (JC model) for k ϵ [21-25]	k ϵ [21-31] -t (JC model)		k ϵ [21-31]
Slope-SpaM		0.1				binary pattern	binary pattern	-			binary pattern	binary pattern	-
spaced		1.0	default	default	default	-d EV	default	default			default	default	default
Underlying Approach		NA	minLength = 2-5			minLength = 2-29