MAUVEALIGNER(1)

💖 MAUVEALIGNER 💖

okay bestie, sit down, hydrate, and let me tell you about mauveAligner — it lives in section 1 of the manual (User Commands, yk, the command-line girlies), and it's all about efficiently constructing multiple genome alignments. no cap. it's giving "I align whole genomes for breakfast" and honestly? obsessed. 💅

✨ SYNOPSIS ✨

mauveAligner [options] <seq1 filename> <sml1 filename> ...  <seqN filename> <smlN filename>

so you feed it pairs of filenames — a seq and an sml for each genome — and it does the thing. yes, ... means keep going. as many as you want, queen. 🦋

🌸 DESCRIPTION 🌸

the mauveAligner and progressiveMauve alignment algorithms have been implemented as command-line programs, and they ship with the downloadable Mauve software. 📦

when you run them from the command line, these programs give you options that are not yet available in the graphical interface. so yeah — the CLI is lowkey the VIP section. the GUI could never. 👑

🎀 OPTIONS 🎀

• --output=<file> — output file name. by default it just prints to screen, which is cute for tiny stuff but not for your 40-genome situation, bestie.
• --mums — find MUMs only, and do not attempt to determine locally collinear blocks (LCBs). just the MUMs. nothing else. keep it simple. 🍓
• --no-recursion — don't perform recursive anchor identification. heads up: this implies --no-gapped-alignment.
• --no-lcb-extension — if you're determining LCBs, don't attempt to extend the LCBs. leave them exactly as they are. no glow-up for them. 🙈
• --seed-size=<number> — initial seed match size. default is log_2( average seq. length ). math girlie behavior, love that for us. 🧮
• --max-extension-iterations=<number> — limit LCB extensions to this number of attempts. default is 4.
• --eliminate-inclusions — eliminate linked inclusions in subset matches. bye bye, inclusions. 💀
• --weight=<number> — minimum LCB weight, measured in base pairs per sequence.
• --match-input=<file> — use the specified match file instead of searching for matches. you already did the work, so skip the search. 💅
• --lcb-match-input — indicates that the match input file contains matches that have been clustered into LCBs.
• --lcb-input=<file> — use the specified lcb file instead of constructing LCBs (this skips LCB generation entirely). 🏃♀️
• --scratch-path=<path> — for large genomes, use a directory for storage of temporary data. Should be given two or more times to with different paths.
• --id-matrix=<file> — generate LCB stats and write them to the specified file.
• --island-size=<number> — find islands larger than the given number.
• --island-output=<file> — output islands the given file (requires --island-size).
• --backbone-size=<number> — find stretches of backbone longer than the given number of b.p.
• --max-backbone-gap=<number> — allow backbone to be interrupted by gaps up to this length in b.p.
• --backbone-output=<file> — output islands the given file (requires --island-size).
• --coverage-output=<file> — output a coverage list to the specified file (use - for stdout). ✨
• --repeats — generates a repeat map. Only one sequence can be specified when you do this. one. singular. don't push it. 🚨
• --output-guide-tree=<file> — write out a guide tree to the designated file. 🌳
• --collinear — assume that input sequences are collinear — they have no rearrangements.

🫶 Gapped alignment controls

• --no-gapped-alignment — don't perform a gapped alignment.
• --max-gapped-aligner-length=<number> — maximum number of base pairs to attempt aligning with the gapped aligner.
• --min-recursive-gap-length=<number> — minimum size of gaps that Mauve will perform recursive MUM anchoring on (Default is 200).

🌈 Signed permutation matrix options

• --permutation-matrix-output=<file> — write out the LCBs as a signed permutation matrix to the given file.
• --permutation-matrix-min-weight=<number> — a permutation matrix will be written for every set of LCBs with weight between this value and the value of --weight.

👑 Alignment output options

• --alignment-output-dir=<directory> — outputs a set of alignment files (one per LCB) to a given directory.
• --alignment-output-format=<directory> — selects the output format for --alignment-output-dir.
• --output-alignment=<file> — write out an XMFA format alignment to the designated file.

supported alignment output formats are: phylip, clustal, msf, nexus, mega, codon. pick your fighter. ⭐

💀 quick vibe check: --no-recursion pulls --no-gapped-alignment in with it whether you asked or not, --island-output and --backbone-output both need --island-size to be around, and --repeats only tolerates one sequence. respect the boundaries, bestie.

and that's the whole page, fr fr — this is mauveAligner version 1.2.0+4713, from April 2015, and it remains iconic. periodt. 💖✨🎀