ANDI(1)

💖 ANDI(1) · the andi manual 💖

🦋 NAME 🦋

andi - estimates evolutionary distances ✨

🧚 SYNOPSIS 🧚

andi [OPTIONS...] FILES...

🌸 DESCRIPTION 🌸

okay so andi is the tool you reach for when you need to estimate how far apart closely related genomes are 🧬 It reads your input sequences from FASTA files and computes the pairwise anchor distance for each pair. The whole idea is explained in a paper by Haubold et al. (2015), and honestly it's giving main character energy 💅

💜 OUTPUT 💜

The output is a symmetrical distance matrix in PHYLIP format 📊 Every entry is a divergence written as a positive real number. A distance of 0 means the two sequences are identical 🫶 Any other value is an estimate of the nucleotide substitution rate, Jukes-Cantor corrected ✨

Sometimes the comparison just fails and no estimate can be computed, and in that case nan gets printed 💀 That happens when the input sequences were either too short (<200bp) or too diverse (K>0.5) for the method to work properly. Not me being sad about it, but yeah, that's the deal 😭

🎀 OPTIONS 🎀

• -b INT, --bootstrap=INT — computes multiple distance matrices, with n-1 bootstrapped from the first one 🌈 For the full scoop, check out the paper Klötzl & Haubold (2016).
• --file-of-filenames=FILE — usually you'd pass the filenames as commandline arguments, but with this one you can read them from a file instead, one name per line 📝 Use a single dash ('-') to read from stdin.
• -j, --join — use this mode if each of your FASTA files is one assembly with a bunch of contigs 🧩 andi will treat all the sequences in a file as a single genome. In this mode you need at least one filename passed via command line arguments. For the output, the filename is what identifies each sequence 🏷️
• -l, --low-memory — in multithreaded mode, andi needs memory that scales linearly with the number of threads 📈 Low memory mode flips that to a constant memory demand, no matter how many threads you use. The catch? It comes at a significant runtime cost 🐢 ngl a tradeoff, but a valid one.
• -m MODEL, --model=MODEL — sets the nucleotide evolution model to one of 'Raw', 'JC', 'Kimura', or 'LogDet' 💅 By default, the Jukes-Cantor correction is used.
• -p FLOAT — significance of an anchor. The default is 0.025 ✨
• --progress[=WHEN] — prints a progress bar 📊 WHEN can be 'auto' (the default if you leave it out), 'always', or 'never'.
• -t INT, --threads=INT — the number of threads to use. By default, all available processors get put to work 🔥 Multithreading is only available if andi was compiled with OpenMP support, so check that first 🙈
• --truncate-names — by default andi outputs the full names of sequences, and names shorter than ten characters get padded with spaces 🌷 Names longer than ten characters can cause problems with downstream tools, so if that's you, this switch truncates them.
• -v, --verbose — prints additional information, including the amount of homology that was found 🔍 Apply it multiple times for extra verboseness, because more is sometimes more 🤭
• -h, --help — prints the synopsis and an explanation of the available options 🫶
• --version — outputs version information and acknowledgments 🌈

🌈 COPYRIGHT 🌈

Copyright © 2014 - 2021 Fabian Klötzl, License GPLv3+: GNU GPL version 3 or later 💜 This is free software, so you're free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law 🙈 The full license text lives at <http://gnu.org/licenses/gpl.html>.

🧠 ACKNOWLEDGMENTS 🧠

Big thanks to the people who made all this possible 🫶

1. andi: Haubold, B. Klötzl, F. and Pfaffelhuber, P. (2015). andi: Fast and accurate estimation of evolutionary distances between closely related genomes, Bioinformatics 31.8.
2. Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f.
3. SA construction: Mori, Y. (2005). libdivsufsort, unpublished.
4. Bootstrapping: Klötzl, F. and Haubold, B. (2016). Support Values for Genome Phylogenies, Life 6.1.

🐛 BUGS 🐛

Reporting Bugs

Please report bugs to <kloetzl@evolbio.mpg.de> or at <https://github.com/EvolBioInf/andi> 🥺 We love a good bug report bestie 💖

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Version 0.14, dated 2020-01-09, and the man page itself is ANDI(1). Stay iconic, bestie 🦋✨