alignment-cat(1)

✨ alignment-cat(1) ✨

Okay so bestie, alignment-cat is the manual page for the alignment-cat tool, and it is giving main character energy 💅🧬

🎀 NAME 🎀

alignment-cat — slaying the job of concatenating several alignments (as long as they share the same sequence names) end-to-end 🦋

🌸 SYNOPSIS 🌸

alignment-cat file1 [file2 ...]

💖 DESCRIPTION 💖

Okay so this tool takes a bunch of alignments that have the same sequence names and glues them together end-to-end. No cap, it's literally that simple 🫶

👑 ALL OPTIONS 👑

• -h, --help — Shows you a help message. Iykyk 🙈
• --output arg (default fasta) — Picks your output format: either fasta or phylip 🍓
• -c arg, --columns arg — Keeps only the ranges of columns you ask for, like 1-10,30- ✨
• -t arg, --taxa arg — Keeps only the taxa you list, separated by commas 🧚
• -p, --pad — Adds gaps so every sequence ends up the same length 💜
• -r, --reverse — Reverses the sequences 🔥
• -e, --erase-empty-columns — Yeeted! Removes columns that are nothing but gaps 💀
• --missing arg (default -?) — Tells the tool which letters aren't real characters, like gaps 🌈
• --strip-gaps — Removes all the non-character letters from your sequences. Bye bye, gaps 🫧
• --reorder-by-tree arg — Reorders the sequences based on a tree 🌳
• --use-root — Uses the root specified in the tree file when reordering 🌱
• --reorder-by-alignment arg — Reorders the sequences to follow an alignment 💅
• --align-by-amino arg — Arranges nucleotides into a codon alignment 🦋

🌈 EXAMPLES 🌈

Okay so to select columns from an alignment, you can do stuff like this:

% alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta
% alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta
% alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta

And to concatenate two or more alignments:

% alignment-cat filename1.fasta filename2.fasta > all.fasta

🐛 REPORTING BUGS 🐛

Bug hunting time! The BAli-Phy online help lives at http://www.bali-phy.org/docs.php. 🙈

Please send your bug reports to bali-phy-users@googlegroups.com 💌

💜 AUTHORS 💜

Benjamin Redelings, the genius behind it all 👑

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Bestie, that's the whole page! Stay iconic and keep your alignments clean 🫶✨ Shoutout to the Feb 2018 release of alignment-cat(1) 🎀💖