InformationDistances

This package contains methods to calculate the Normalized Compression Distance (NCD) - a metric for measuring how similar two strings are using a real life compression algorithm such as bzip2.

Installation

InformationDistances.jl is registered in the general registry and can therefore be simply installed from the REPL with

] add InformationDistances

Quick example

julia> using InformationDistances

# Create three strings that we want to compare - we expect s1 and s2 to be more similar than any of them to s3
julia> s1 = repeat("ab", 100)
"abababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababab"

julia> s2 = repeat("ba", 100)
"babababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababababa"

julia> s3 = String(rand(('a', 'b'), 200))
"aabaaabaaababaabababbaaaaabaaaaaabbabbaaabbbabbbbaaaaababaabbbbaababbbbaaaaaaaaabababaaabbbbbbbabbbaabbabababbaababbbbabbbababaaaababaaababbababaaaaababbabbbbaabbaabbbaabaababbbaaaaaababbbabbbabbabbaa"

# Create a normalized compression distance with the default parameters
julia> d = NormalizedCompressionDistance();

julia> d(s1, s2)
0.125

julia> d(s1, s3)
0.4482758620689655

julia> d(s2, s3)
0.4482758620689655

# Create annother distance that uses Bzip2 for compression
julia> using CodecBzip2: Bzip2Compressor

julia> d_bzip2 = NormalizedCompressionDistance(CodecCompressor{Bzip2Compressor}(workfactor=250));

julia> d_bzip2(s1, s2)
0.1

julia> d_bzip2(s1, s3)
0.5903614457831325

julia> d_bzip2(s2, s3)
0.5783132530120482

Example Notebooks

The examples folder contains an interactive notebook that can be run with Pluto.jl. To quickly view the notebook online there is also a static non-interactive version where it is currently not possible to choose different options.

• mitochondrial-enome-phylogency.jl       non interactive version

References

Li, Ming, Xin Chen, Xin Li, Bin Ma, and Paul MB Vitányi. "The similarity metric." IEEE transactions on Information Theory 50, no. 12 (2004): 3250-3264.