POPULATIONS(1)

✨ POPULATIONS 💖

okay bestie, welcome to the populations User Manual 🌸 like, this is the actual documentation for populations, and I'm about to make it make sense for you. no cap.

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🦋 NAME

populations — population genetic software 💅

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🌈 SYNOPSIS

populations

populations [name_of_input_file] [option]

You can use populations as a command line program (super useful for batch treatment, fr fr) to infer phylogenetic trees. 🌳

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💜 DESCRIPTION

So populations is a population genetic software. It computes genetic distances between populations or individuals, and it builds phylogenetic trees (NJ or UPGMA) with bootstrap values. That's the whole vibe. ✨

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👑 FEATURES

• haploids, diploids or polyploids genotypes (see input formats) 🧬
• structured populations (see input files structured populations
• No limit of populations, loci, alleles per loci (see input formats) — no ceiling, we love that for us
• Distances between individuals (15 different methods)
• Distances between populations (15 methods)
• Bootstraps on loci OR individuals
• Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format) 🌳
• Allelic diversity
• Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations...)

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💅 OPTIONS

• -phylogeny ind|pop — (default) for phylogenetic trees based on individuals or populations. pick your fighter 🫶
• dist method — (default: Nei standard, Ds) you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. see distances for details. (yes Dr shows up twice, that's literally what it says, don't come for me 😭)
• -construct method — (default: upgma) possibilities upgma or nj (Neighbor Joining)
• -bootstrap_ind n — number to indicate the number of bootstraps to perform on individuals
• -bootstrap_locus n — number to indicate the number of bootstraps to perform on loci
• -output name_of_treeview_file — to indicate the name of the tree file (phylip tree format)
• -level n — number, structured populations allows to choose the structuration factor (in the example: town level is 1, building level is 2...). it's giving nested vibes 🪆

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🎀 EXAMPLE

populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus 10000 -output toutc2_10000_Dm.tre

Commands can be write in a .bat file (for DOS) or a script file (for UNIX) ⭐

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🌸 AUTHOR

Georges Khaznadar <georgesk@ofset.org> Wrote this manpage for the Debian system.

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💖 COPYRIGHT

Copyright © 2011 Georges Khaznadar

This manual page was written for the Debian system (and may be used by others).

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version published by the Free Software Foundation.

On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

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and that's the whole page bestie 🫶 this one came from the populations source, dated 06/19/2011, sitting pretty in section POPULATIONS(1) of the manual. go build some trees, you absolute icon 👑💅