SPACED(1)

💖 SPACED(1) — the spaced girlies' manual 💖

okay so bestie, buckle up, we're talking about spaced — alignment-free sequence comparison. yes, it's the spaced command, manual section 1, and no, we are NOT being boring about it. 🦋

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✨ NAME ✨

spaced — alignment-free sequence comparison 🧬

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🌸 SYNOPSIS 🌸

spaced [-r] [-k INT] [-l INT] [-n INT] [-t INT] [-d TYPE] [-f FILE]
FILES...

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🎀 DESCRIPTION 🎀

Spaced Words is a whole new approach to alignment-free sequence comparison, and honestly? it's giving main character energy. 💅

so most alignment-free algorithms out there are out here comparing the word-composition of sequences. cute. but Spaced Words said "not me" and instead uses a pattern of care and don't care positions. 🫶

here's the vibe: the occurrence of a spaced word in a sequence is defined by the characters at the match positions only — the characters at the don't care positions are literally ignored, no cap. (this was originally inspired by the PatternHunter algorithm for homology search in databases, iykyk.)

so 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. then an information-theoretic distance measure is used to define pairwise distances on the set of input sequences, based on their spaced-word frequencies. 🔥

the original version of this spaced-words approach was published in Boden et al. (2013). iconic. periodt.

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🌈 OUTPUT 🌈

the output is a symmetrical distance matrix similar to PHYLIP format, with each entry representing divergence as a positive real number. ⭐

• a distance of zero means two sequences are identical
• other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected)

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✨ OPTIONS ✨

• -o <file> — print the distance matrix to the given file. default is DMat. 💾
• -k <int> — set the pattern's weight. default: 14.
• -l <int> — set don't care positions for the used patterns. default: 15.
• -n <int> — set the number of patterns. default: 5.
• -f <file> — instead of generating new patterns, read them from the given file. 📂
• -t <INT> — the number of threads to be used; by default, 25 threads are used. multithreading is only available if spaced was compiled with OpenMP support. 🧵

bestie listen. if your build doesn't have OpenMP, that -t is gonna do absolutely nothing for you. check before you complain, fr fr.

• -r — skip comparison with the reverse complement. 🙈
• -d <type> — the distances can be computed with different measures. available options are:
  • Euclidean (EU)
  • Jensen-Shannon (JS)
  • evolutionary distance (EV)

default: EV.

• -h — prints the synopsis and an explanation of available options. the little help menu that could. 👑

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👑 COPYRIGHT 👑

Copyright © 2016 Chris Leimeister <chris.leimeister@stud.uni-goettingen.de> License GPLv3+: GNU GPL version 3 or later.

This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. the full license text is available at <http://gnu.org/licenses/gpl.html>. 📜

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📚 REFERENCES 📚

1. C.-A. Leimeister, M. Boden, S. Horwege, S. Lindner, B. Morgenstern (2014). Fast alignment-free sequence comparison using spaced-word frequencies, Bioinformatics <http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu177>
2. S. Horwege, S. Linder, M. Boden, K. Hatje, M. Kollmar, C.-A. Leimeister, B. Morgenstern (2014). Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches, Nucleic Acids Research 42, W7-W11 <http://nar.oxfordjournals.org/content/42/W1/W7.abstract>
3. B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015). Estimating evolutionary distances between genomic sequences from spaced-word matches, Algorithms for Molecular Biology 10,5

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💀 BUGS 💀

Reporting Bugs 🐛

please report bugs to <kloetzl@evolbio.mpg.de> or <chris.leimeister@stud.uni-goettingen.de>. they're nice, they wanna hear from you, be brave. 🫶

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version 1.0.2, February 2016 — that's the tea, bestie. now go align something alignment-free. mwah 💋✨