Alignment-free tools

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
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