CLMORDER(1)

💖 clm order — the manual, but make it cute 💖

okay bestie, so this is clm_order from the clm family of user commands, and it's giving reorder clusterings conformal to inclusion structure ✨

real talk though — clmorder is not actually a program, no cap. this page is just documenting what happens when the clm program gets invoked in mode order. and heads up: the options -h, --apropos, --version, -set, --nop are accessible in all clm modes, and they're described over in the clm manual page, not here 💅

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✨ SYNOPSIS ✨

clm order [-prefix <string> (file multiplex prefix)] [-o <fname>
(concatenated output in single file)] <cluster|stack>+

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🦋 DESCRIPTION 🦋

so here's the vibe 🫶 — give clm order a set of input clusterings and the very first thing it does is transform that into a stack of strictly nesting clusterings, by splitting clusters where it has to. no biggie.

then it reorders the coarsest clustering — that's the level-one one — going from large to small clusters 🔥

after that it reorders the second coarsest clustering conformally, which means the first batch among its reordered clusters covers the level-one largest cluster, the second batch covers the level-one second largest cluster, and so on forever and ever 🌈

and within those constraints, each batch of second-level clusters (each one corresponding to a single first-level cluster) gets ordered from larger to smaller clusters again. this whole thing is applied recursively throughout the entire stack of input clusters. it's giving fractal energy fr fr 💫

okay so about input and output 📝 — the input can be specified in multiple files, and a single file may contain multiple clusterings. the output is by default written as a concatenation of matrix files, aka the so-called stack format. use the -o option if you want to specify the output file. and if you want to convert the stacked format to Newick format, you go use mcxdump(1) 💖

you can also write the output to multiple files, one for each projected clustering, by using the -prefix option. like for example, -prefix P leads to output in files named P1, P2, ..PN, where N is the number of clusters in the input, P1 is the most fine-grained ordered clustering, and PN is the coarsest clustering 👑

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🎀 OPTIONS 🎀

• -prefix (<string>) — as described above, bestie. sets the file multiplex prefix.
• -o (<fname>) — as described above. puts the concatenated output in a single file.

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👑 AUTHOR 👑

Stijn van Dongen. (an icon, honestly)

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🌸 SEE ALSO 🌸

mclfamily(7) — for an overview of all the documentation and the utilities in the mcl family. go read it, it's the whole lore 💜

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and that's the whole page, bestie!! this was clm order 22-282, dated 9 Oct 2022, and it lives under clm order(1) in the USER COMMANDS section 🎀✨ bye ily 🫶