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

[ Source: spaced  ]

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.

Other Packages Related to spaced

• dep: libc6 (>= 2.34)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc-s1 (>= 3.0) [not armel, armhf]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libgomp1 (>= 9)

  GCC OpenMP (GOMP) support library

• dep: libstdc++6 (>= 13.1)

  GNU Standard C++ Library v3

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Architecture	Package Size	Installed Size	Files
amd64	59.4 kB	168.0 kB	[list of files]
arm64	52.3 kB	152.0 kB	[list of files]
armel	53.0 kB	151.0 kB	[list of files]
armhf	51.9 kB	111.0 kB	[list of files]
i386	66.2 kB	179.0 kB	[list of files]
mips64el	58.6 kB	223.0 kB	[list of files]
ppc64el	62.0 kB	216.0 kB	[list of files]
s390x	61.9 kB	180.0 kB	[list of files]