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[ Source: spaced  ]

Package: spaced (1.2.0-201605+dfsg-4)

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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 spaced

Download for all available architectures
Architecture Package Size Installed Size Files
alpha (unofficial port) 58.3 kB216.0 kB [list of files]
amd64 59.4 kB168.0 kB [list of files]
arm64 52.3 kB152.0 kB [list of files]
armel 53.0 kB151.0 kB [list of files]
armhf 51.9 kB111.0 kB [list of files]
hppa (unofficial port) 63.5 kB165.0 kB [list of files]
i386 66.2 kB179.0 kB [list of files]
ia64 (unofficial port) 73.9 kB301.0 kB [list of files]
m68k (unofficial port) 59.2 kB167.0 kB [list of files]
mips64el 58.6 kB223.0 kB [list of files]
ppc64 (unofficial port) 62.4 kB216.0 kB [list of files]
ppc64el 62.0 kB216.0 kB [list of files]
riscv64 57.7 kB128.0 kB [list of files]
s390x 61.9 kB180.0 kB [list of files]
sh4 (unofficial port) 72.2 kB215.0 kB [list of files]
sparc64 (unofficial port) 51.0 kB1,050.0 kB [list of files]
x32 (unofficial port) 59.0 kB159.0 kB [list of files]