SEQAN_TCOFFEE(1)

💖 SEQAN_TCOFFEE 💖

okay bestie, so this is the seqan_tcoffee manual page — yes, that's the manual name, SEQAN_TCOFFEE(1), section 1, we're in the big leagues now 🫶 — and it's literally all about multiple sequence alignment. Buckle up, it's giving bioinformatics excellence ✨

🎀 NAME 🎀

seqan_tcoffee — multiple sequence alignment 💅

🌸 SYNOPSIS 🌸

seqan_tcoffee -s <FASTA FILE> [OPTIONS]

✨ DESCRIPTION ✨

seqan2::T-Coffee is a multiple sequence alignment tool. That's the whole vibe. It aligns your sequences, it does it well, periodt. 👑

Also hi, a little legal moment: (c) Copyright 2009 by Tobias Rausch — respect the author, always 🫶

---

💅 OPTIONS 💅

🌈 Universal Basics

• -h, --help — shows you the help message, aka the "what do I even do here" button. Use it, no shame 🙈
• --version — tells you what version you're running. Info, but make it fashion ⭐

👑 Main Options

• -s, --seq INPUT_FILE — the name of your multi-fasta input file. Valid filetypes are: .frn, .fna, .ffn, .fasta, .fas, .faa, and .fa. Basically your starting lineup 💖
• -a, --alphabet STRING — which sequence alphabet you're working with. One of protein, dna, rna, and iupac. Default: protein. Yes bestie, it assumes protein unless you say otherwise 🧚
• -o, --outfile OUTPUT_FILE — the name of your output file. Valid filetypes are: .msf, .frn, .fna, .ffn, .fasta, .fas, .faa, and .fa. Default: out.fasta. Your results gotta go somewhere 🌸

🦋 Segment Match Generation Options

• -m, --method List of STRING's — defines the generation method for matches. Want multiple generation methods? Recall this option with different arguments, one at a time, like the icon you are. One of global, local, overlap, and lcs. Default: global and local. Slay 🎀
• -l, --libraries List of INPUT_FILE's — name of match file. Same deal: multiple files means recalling this option with different arguments. Valid filetypes are: .mums, .lib, .blast, and .aln 📚
• -pa, --pairwise-alignment STRING — pairwise alignment method. Default: unbanded for usual alignments (fewer than 50 sequences), banded for deep alignments (50 sequences or more). One of unbanded and banded. It literally reads the room 🔥
• -bw, --band-width INTEGER — band width. This option automatically selects banded pairwise alignment (see pa for details). In range [2..inf]. Default: 60. Wide band, wide energy ✨

💜 Scoring Options

• -g, --gop INTEGER — gap open penalty. Default: -13. Ouch, that's a real penalty 😭
• -e, --gex INTEGER — gap extension penalty. Default: -1.
• -ma, --matrix STRING — score matrix. Default: Blosum62.
• -ms, --msc INTEGER — match score. Default: 5.
• -mm, --mmsc INTEGER — mismatch penalty. Default: -4.

🌈 Guide Tree Options

• -u, --usetree STRING — name of the file containing the Newick Guide Tree 🌳
• -b, --build STRING — method to build the tree. Following methods are provided: Neighbor-Joining (nj), UPGMA single linkage (min), UPGMA complete linkage (max), UPGMA average linkage (avg), UPGMA weighted average linkage (wavg). Neighbor-Joining creates an unrooted tree, which we root at the last joined pair. One of nj, min, max, avg, and wavg. Default: nj. Tree drama, but make it algorithmic 👑

⭐ Alignment Evaluation Options

• -i, --infile INPUT_FILE — name of the alignment file <FASTA FILE>. Valid filetypes are: .frn, .fna, .ffn, .fasta, .fas, .faa, and .fa. Time to grade your own work 📝

---

ok so real talk, one tiny thing: if you want more than one value for -m/--method or -l/--libraries, you don't stack them in one go — you recall the option with different arguments. That's just the move, iykyk 💖

and that's the whole page bestie, every single flag accounted for, nothing skipped, no cap 🫶

---

this has been seqan_tcoffee version 1.13.12 [tarball], from the SEQAN_TCOFFEE(1) manual — mwah, go align something iconic 💅✨