PC-COMPARE(1)

💖 PC-COMPARE(1) 💖

okay so bestie, you're in the Probcons Manual and this is the page for pc-compare. grab a snack, we're scoring alignments 🫶

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✨ NAME ✨

pc-compare — a program for scoring alignments according to a reference alignment, with respect to sum-of-pairs and column scores. that's the whole vibe. it compares, it scores, it slays 💅

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🌸 SYNOPSIS 🌸

pc-compare [TEST_ALIGNMENT] [REFERENCE_ALIGNMENT] [BALIBASE_ANNOT_FILE]
           [-col] [-core] [-caps] [-annot FILENAME]

so you hand it a test alignment, a reference alignment, and optionally a balibase annotation file, and then there's a little pile of flags: -col, -core, -caps, and -annot FILENAME. that's it, that's the whole invocation. no cap 🧚

ngl the page itself doesn't spell out what each flag does beyond the synopsis, so i'm not gonna make stuff up — the command line above is the tea, fr fr. 🙈

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⭐ NOTE ⭐

okay important lore: pc-compare is named compare in the original sources. it got renamed so it wouldn't collide with other program names. iconic decision honestly, the way that naming collisions are a whole thing 👑

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🦋 SEE ALSO 🦋

• pc-makegnufile(1) — from the probcons-extra package
• pc-project(1) — also from the probcons-extra package
• probcons(1) — from the probcons package
• probcons-RNA(1) — from the probcons package

go read those too, bestie, the whole friend group is cute 🌈

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💜 REFERENCE 💜

please cite this, it's the polite thing to do:

Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.

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👑 AUTHORS 👑

• Chuong Do <chuongdo@cs.stanford.edu>
  • wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University. academic main character energy fr ✨
• Charles Plessy <charles-debian-nospam@plessy.org>
  • wrote this manpage in DocBook XML for the Debian distribution. a legend, truly 🎀

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💀 COPYRIGHT 💀

this program and its manpage are in the public domain. free as a butterfly, no strings, go wild 🦋

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okay bye bestie, that was pc-compare version 1.12, dated 2007-04-04 — thank you for coming to my ted talk, mwah 💖💅