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[ Source: spaced  ]

Package: spaced (1.2.0-201605+dfsg-1)

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alignment-free sequence comparison using spaced words

Spaced (Words) is a new approach to alignment-free sequence comparison. While most alignment-free algorithms compare the word-composition of sequences, spaced uses a pattern of care and don't care positions. The occurrence of a spaced word in a sequence is then defined by the characters at the match positions only, while the characters at the don't care positions are ignored. Instead of comparing the frequencies of contiguous words in the input sequences, this new approach compares the frequencies of the spaced words according to the pre-defined pattern. An information-theoretic distance measure is then used to define pairwise distances on the set of input sequences based on their spaced-word frequencies. Systematic test runs on real and simulated sequence sets have shown that, for phylogeny reconstruction, this multiple-spaced-words approach is far superior to the classical alignment-free approach based on contiguous word frequencies.

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Download for all available architectures
Architecture Package Size Installed Size Files
amd64 55.7 kB161.0 kB [list of files]
arm64 50.1 kB137.0 kB [list of files]
armel 47.9 kB132.0 kB [list of files]
armhf 48.6 kB96.0 kB [list of files]
i386 63.1 kB168.0 kB [list of files]
mips 57.8 kB178.0 kB [list of files]
mips64el 56.9 kB184.0 kB [list of files]
mipsel 58.9 kB178.0 kB [list of files]
ppc64el 59.4 kB209.0 kB [list of files]
s390x 51.4 kB161.0 kB [list of files]