ALF(1)

📦
version 2.5.2 · 2 versions
, in ubuntu stonking

👑 ALF(1) — the alignment-free sequence comparison era 💅

okay bestie, welcome to alf, the manual page for ALF version 1.1.14 — Alignment free sequence comparison. No alignments, no drama, just vibes and k-mer math. Let's get into it 🦋

✨ NAME ✨

alf — Alignment free sequence comparison

🌸 SYNOPSIS 🌸

alf [OPTIONS] -i IN.FASTA [-o OUT.TXT]

💖 DESCRIPTION 💖

So what this does is: it computes the pairwise similarity of sequences using alignment-free methods from the file IN.FASTA, and then writes out a tab-delimited matrix with pairwise scores to OUT.TXT. That's it, that's the whole glow-up ✨ — no aligning, just counting.

🎀 OPTIONS 🎀

🫶 The basics

  • -h, --help — shows you the help message. classic. iconic. your first stop.
  • --version — spills the version info.
  • -v, --verbose — when you give it, all the details about the progress get printed to the screen. not me wanting to see everything happen live 💀

🍓 Input / Output

🌈 -i, --input-file INPUT_FILE

The name of the multi-FASTA input file. valid filetypes are:

.sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*],
.ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*],
.embl[.*], and .bam

where * is any of these extensions: gz, bz2, and bgzf, so you get transparent (de)compression. it's giving flexible 💅

🌟 -o, --output-file OUTPUT_FILE

The name of the file where that tab-delimited matrix with pairwise scores gets written. default is to write to stdout, so if you're a "just pipe it somewhere" girlie that's your moment. valid filetype is: .alf[.*], where * is any of the following extensions: tsv for transparent (de)compression.

🧚 General Algorithm Parameters

⭐ -m, --method STRING

Pick the method to use. one of N2, D2, D2Star, and D2z. default: N2.

💜 -k, --k-mer-size INTEGER

The size of the k-mers. default: 4.

🌸 -mo, --bg-model-order INTEGER

The order of the background Markov Model. default: 1.

👑 N2 Algorithm Parameters

these ones are specifically for the N2 method, so if you're using another method they don't really eat here. proceed accordingly 🙈

🦋 -rc, --reverse-complement STRING

Which strand to score. use both_strands to score both strands simultaneously (main character energy, doing both at once). one of input, both_strands, mean, min, and max. default: input.

💀 -mm, --mismatches INTEGER

Number of mismatches, one of 0 and 1. when 1 is used, N2 uses the k-mer-neighbour with one mismatch. default: 0.

🎀 -mmw, --mismatch-weight DOUBLE

A real-valued weight of counts for words with mismatches. default: 0.1.

✨ -kwf, --k-mer-weights-file OUTPUT_FILE

Prints the k-mer weights for every sequence to this file if you give it. valid filetype is: .txt.

💌 CONTACT AND REFERENCES

Got questions or comments? slide into the inbox:

Jonathan Goeke <goeke@molgen.mpg.de>

Also fr fr please reference this publication if you used ALF or the N2 method for your analysis:

Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin
Vingron. Estimation of Pairwise Sequence Similarity of Mammalian
Enhancers with Word Neighbourhood Counts. Bioinformatics (2012).

Project Homepage:

https://www.seqan.de/apps/alf

okay that's the whole page bestie, you're officially ALF-literate 🫶 go forth and compare your sequences alignment-free, no cap. this was alf 1.1.14 [tarball], and you've been reading ALF(1) — stay iconic, mwah 💖✨

📦 where this page comes from