Table 1 Alignment-free sequence comparison tools included in this study

AAF [38]

Exact k-mer count

10/01/2017

https://github.com/fanhuan/AAF

AFKS [34]

1.0

https://github.com/TulsaBioinformaticsToolsmith/Alignment-Free-Kmer-Statistics

alfpy [5]

1.0.6

https://github.com/aziele/alfpy

CAFÉ [36]

1.0.0

https://github.com/younglululu/CAFE

FFP [35, 39]

2v.2.1

https://github.com/jaejinchoi/FFP

jD2Stat [37]

1.0

http://bioinformatics.org.au/tools/jD2Stat/

LZW-Kernel [40]

Information theory

NA

https://github.com/kfattila/LZW-Kernel

spaced [41,42,43]

Inexact k-mer count

1.0

http://spaced.gobics.de

kWIP [44]

k-mer count

0.2.0–13-g3cf8a9e

https://github.com/kdmurray91/kWIP

ALFRED-G [45]

Maximal length of exact common substrings

NA

https://alurulab.cc.gatech.edu/phylo

kmacs [20, 42]

1.0

http://kmacs.gobics.de

kr [46]

2.0.2

http://guanine.evolbio.mpg.de/cgi-bin/kr2/kr.cgi.pl

Underlying Approach [47]

NA

http://www.dei.unipd.it/~ciompin/main/underlying.html

andi [24]

Micro-alignments

0.02

https://github.com/EvolBioInf/andi

co-phylog [23]

NA

https://github.com/yhg926/co-phylog

FSWM [26]/Read-SpaM [48]

1.0

http://fswm.gobics.de

Multi-SpaM [25]

1.0

https://github.com/tdencker/multi-SpaM

phylonium [49]

0.3

https://github.com/kloetzl/phylonium

mash [11]

Number of word matches

2.1

https://github.com/marbl/Mash

Slope-SpaM

0.1

https://github.com/burkhard-morgenstern/Slope-SpaM

Skmer [50]

3.0.0

https://github.com/shahab-sarmashghi/Skmer

RTD-Phylogeny [51]

Return time distribution

1.0.1

https://github.com/pandurang-kolekar/rtd-phylogeny

kSNP3 [52]

SNP count

3.1

https://sourceforge.net/projects/ksnp/files/

EP-sim [53]

Variable-length word counts

1.0

http://www.dei.unipd.it/~ciompin/main/EP-sim.html