alignment-thin(1)

✨ NAME ✨

Okay bestie, alignment-thin(1) is the declutter queen 👑 It's how you remove sequences or columns from an alignment 🦋

🌸 SYNOPSIS 🌸

alignment-thin alignment-file [OPTIONS]

💖 DESCRIPTION 💖

Literally all it does is yeet sequences or columns out of an alignment. Slay ✨

🎀 GENERAL OPTIONS 🎀

• -h, –help — Shows you the usage info 🧚
• -V, –verbose — Gives you extra log messages on stderr, for when you need the tea ☕

🦋 SEQUENCE FILTERING OPTIONS 🦋

• -p arg, –protect arg — These sequences are untouchable and can't be removed. Pass them as a comma-separated list 🛡️
• -k arg, –keep arg — Removes every sequence that is not in the comma-separated list arg 🫶
• -r arg, –remove arg — Removes the sequences in the comma-separated list arg 💅
• -l arg, –longer-than arg — Removes sequences that aren't longer than arg 📏
• -s arg, –shorter-than arg — Removes sequences that aren't shorter than arg 📐
• -c arg, –cutoff arg — Removes similar sequences where the number of mismatches is less than cutoff 🔥
• -d arg, –down-to arg — Keeps removing similar sequences until only arg sequences are left 🌈
• –remove-gappy arg — Yeets arg outlier sequences. These are the ones that are missing too many conserved sites 🙈
• –conserved arg (=0.75) — The fraction of sequences that have to contain a letter before that spot counts as conserved. The default is 0.75 💜

🌈 COLUMN FILTERING OPTIONS 🌈

• -K arg, –keep-columns arg — Keeps the columns from this sequence ⭐
• -m arg, –min-letters arg — Removes columns that have fewer than arg letters 🍓
• -u arg, –remove-unique arg — Removes insertions that live in a single sequence if they're longer than arg letters 🧚
• -e, –erase-empty-columns — Removes columns with no characters at all (all gaps) 🫧

👑 OUTPUT OPTIONS 👑

• -S, –sort — Sorts partially ordered columns so similar gaps end up grouped together 🎀
• -L, –show-lengths — Just prints out the sequence lengths and nothing else 📝
• -N, –show-names — Also just prints out sequence lengths, according to the page 🙈

Lowkey sus: the page describes -N with the exact same sentence as -L, so it's listed here exactly as written.

• -F arg, –find-dups arg — For each sequence, finds the closest other sequence 🔍

💅 EXAMPLES 💅

Remove columns without a minimum number of letters:

% alignment-thin --min-letters=5 file.fasta > file-thinned.fasta

Remove sequences by name:

% alignment-thin --remove=seq1,seq2 file.fasta > file2.fasta

% alignment-thin --keep=seq1,seq2   file.fasta > file2.fasta

Remove short sequences:

% alignment-thin --longer-than=250 file.fasta > file-long.fasta

Remove similar sequences with <= 5 differences from the closest other sequence:

% alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta

Remove similar sequences until we have the right number of sequences:

% alignment-thin --down-to=30 file.fasta > file-30taxa.fasta

Remove dissimilar sequences that are missing conserved columns:

% alignment-thin --remove-gappy=10 file.fasta > file2.fasta

Protect some sequences from being removed:

% alignment-thin --down-to=30 file.fasta --protect=seq1,seq2 > file2.fasta

% alignment-thin --down-to=30 file.fasta --protect=@filename > file2.fasta

🐛 REPORTING BUGS 🐛

Need the BAli-Phy online help? It's at http://www.bali-phy.org/docs.php. 🌸

Found a bug? Send it to bali-phy-users@googlegroups.com. We stan bug reports 🫶

🧚 AUTHORS 🧚

Benjamin Redelings. The main character behind it all 👑

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That's the tea, bestie 💖 alignment-thin(1) is from Feb 2018, and it's still giving 🦋✨