Alignment-free tools

Alignment-Free Tools in the Benchmark

Program Submethod Submitter crm protein swisstree assembled ecoli assembled plants unassembled ecoli unassembled plants unsimulated ecoli unsimulated yersinia simulated sim_hgt
AAF A. Zielezinski NA NA NA NA NA
  • k = 12-15, 21, 25-29
  • k = 13-15, 17,20, 24-26
NA NA NA
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
  • H.Girgis
  • B.James
k = 2-6
  • k = 1-3
  • k = 1-3
k = 9-12
  • k = 12-13
  • k = 6-9
  • k = 7-8
  • k = 9-13
  • k = 9-13
  • k = 8-12
alfpy
  • angle_cos_diss
  • angle_cos_evol
  • braycurtis
  • canberra
  • chebyshev
  • google
  • W-metric
A.Zielezinski
  • k = 2-7
  • counts,freqs
  • k = 1-5
  • freqs
  • Wmetric: BLOSUM30-95
  • k = 1-10
  • counts, freqs
  • k = 6-29
  • counts, freqs
  • k = 6-13
  • counts, freqs
NA NA
  • k = 8-29
  • counts, freqs
  • k = 8-20
  • counts, freqs
  • k = 8-29
  • counts, freqs
ALFRED-G A.Zielezinski
  • k = 0-3
  • x = 1-10
  • k = 0-1
  • x = 1-5
  • k = 1
  • x = 1-5
NA NA
  • k = 1
  • x = 10
  • k = 1
  • x = 10
  • k = 0-1
  • x = 1-7
andi A.Zielezinski NA NA NA
  • default
default default default default
CAFE
  • cafe-cvtree
  • cafe-d2shepp
  • cafe-d2star
  • F.Sun
  • K.Tang
  • k = 4-6
NA NA
  • k = 12-13
  • k = 9-12
  • k = 12-13
  • k = 9-11
  • k = 7,12,13
  • k = 6,12,13
  • k = 12,13
co-phylog A.Zielezinski NA NA NA default default default default default
FFP
  • K.Sung-Hou
  • J.Choi
  • A.Zielezinski
  • k = 2-7
  • k = 2-6
  • k = 4-15
  • k = 10-29
  • k = 8-15
  • k = 9-17
  • k = 9-17
  • k = 10-29
  • k = 10-29
  • k = 10-24
FSWM
  • B.Morgenstern
  • C.Leimeister
NA NA NA default default NA NA default default default
jD2Stat
  • d2n
  • D2S
  • D2St
G.Bernard
  • k = 4-10
  • k = 4-10
  • k = 5-10
  • k = 5-26
NA NA NA
  • k = 5-26
  • k = 5-26
  • k = 5-26
kmacs
  • C.Leimeister
  • B.Morgenstern
default default default NA? NA NA default default default
kr A.Zielezinski
  • default
NA NA default NA NA default default default
kSNP3 A.Zielezinski NA NA NA
  • k = 9-15
  • k = 9-12
  • k = 9-12
  • k = 9-12
  • k = 10-13
  • k = 11-18
  • k = 9-12
kWIP A.Zielezinski NA NA NA NA NA
  • k = 9-27
  • k = 11-23
NA NA NA
LZW-Kernel
  • LZW-Kernel
  • LZW-NCD
A.Zielezinski
  • default
  • default
default default
  • default
NA NA default default default
Multi-SpaM
  • C.Leimeister
  • B.Morgenstern
NA NA NA default default default default default default default
Phylonium A.Zielezinski NA NA NA default default default default
RTD-Phylogeny A.Zielezinski
  • k = 1-7
  • k = 1-3
  • k = 1-4
  • k = 1-5
  • k = 1-6
NA NA
  • k = 1-7
  • k = 1-7
  • k = 1-6
spaced
  • C.Leimeister
  • B.Morgenstern
default default default default default NA NA default default default
Underlying Approach A.Zielezinski
  • minLength = 2-5
NA NA NA NA