PROGRESSIVEMAUVE(1)

💖 progressiveMauve — or, how to align a whole squad of genomes 💖

okay bestie, sit DOWN, because progressiveMauve is a whole vibe. It's the PROGRESSIVEMAUVE(1) manual, and it's giving efficiently constructing multiple genome alignments energy. Like, multiple genomes, one alignment, no cap. 🧬✨

🌸 NAME 🌸

progressiveMauve — efficiently constructing multiple genome alignments. that's it, that's the whole thing, she's iconic for it 💅

🦋 DESCRIPTION 🦋

so here's how you talk to her. two modes, depending on how your genomes are chillin':

when each genome resides in a separate file:

progressiveMauve [options] <seq1 filename> ... <seqN filename>

when all genomes are in a single file:

progressiveMauve [options] <seq filename>

periodt. that's the usage. pick your lane 🫶

✨ OPTIONS ✨

every single flag, no gatekeeping, all 38 of them, let's go 🎀

• --island-gap-size=<number> — alignment gaps above this size in nucleotides are considered to be islands. default is [20] 🏝️
• --profile=<file> — (Not yet implemented) read an existing sequence alignment in XMFA format and align it to other sequences or alignments. she's coming, she's just not here yet 🙈
• --apply-backbone=<file> — read an existing sequence alignment in XMFA format and apply backbone statistics to it
• --disable-backbone — backbone detection? disabled. gone. bye 👋
• --mums — find MUMs only, do NOT attempt to determine locally collinear blocks (LCBs)
• --seed-weight=<number> — use the specified seed weight for calculating initial anchors
• --output=<file> — output file name. prints to screen by default 📺
• --backbone-output=<file> — backbone output file name (optional)
• --match-input=<file> — use specified match file instead of searching for matches
• --input-id-matrix=<file> — an identity matrix describing similarity among all pairs of input sequences/alignments
• --max-gapped-aligner-length=<number> — maximum number of base pairs to attempt aligning with the gapped aligner
• --input-guide-tree=<file> — a phylogenetic guide tree in NEWICK format that describes the order in which sequences will be aligned 🌳
• --output-guide-tree=<file> — write out the guide tree used for alignment to a file
• --version — display software version information
• --debug — run in debug mode (perform internal consistency checks--very slow). very slow, bestie, she means it 😭
• --scratch-path-1=<path> — designate a path that can be used for temporary data storage. two or more paths should be specified.
• --scratch-path-2=<path> — designate a path that can be used for temporary data storage. two or more paths should be specified. (yes, you need more than one, the naming is not subtle 💀)
• --collinear — assume that input sequences are collinear--they have no rearrangements
• --scoring-scheme=<ancestral|sp_ancestral|sp> — selects the anchoring score function. default is extant sum-of-pairs (sp).
• --no-weight-scaling — don't scale LCB weights by conservation distance and breakpoint distance
• --max-breakpoint-distance-scale=<number [0,1]> — set the maximum weight scaling by breakpoint distance. defaults to 0.5
• --conservation-distance-scale=<number [0,1]> — scale conservation distances by this amount. defaults to 0.5
• --muscle-args=<arguments in quotes> — additional command-line options for MUSCLE. any quotes should be escaped with a backslash \ 💪
• --skip-refinement — do not perform iterative refinement
• --skip-gapped-alignment — do not perform gapped alignment
• --bp-dist-estimate-min-score=<number> — minimum LCB score for estimating pairwise breakpoint distance
• --mem-clean — set this to true when debugging memory allocations
• --gap-open=<number> — gap open penalty
• --repeat-penalty=<negative|zero> — sets whether the repeat scores go negative or go to zero for highly repetitive sequences. default is negative.
• --gap-extend=<number> — gap extend penalty
• --substitution-matrix=<file> — nucleotide substitution matrix in NCBI format
• --weight=<number> — minimum pairwise LCB score
• --min-scaled-penalty=<number> — minimum breakpoint penalty after scaling the penalty by expected divergence
• --hmm-p-go-homologous=<number> — probability of transitioning from the unrelated to the homologous state [0.00001]
• --hmm-p-go-unrelated=<number> — probability of transitioning from the homologous to the unrelated state [0.000000001]
• --hmm-identity=<number> — expected level of sequence identity among pairs of sequences, ranging between 0 and 1 [0.7]
• --seed-family — use a family of spaced seeds to improve sensitivity 🌱
• --solid-seeds — use solid seeds. do not permit substitutions in anchor matches.
• --coding-seeds — use coding pattern seeds. useful to generate matches coding regions with 3rd codon position degeneracy.
• --disable-cache — disable recursive anchor search cacheing to workaround a crash bug 🐛 (yes, "cacheing", we're keeping the spelling, it's hers)
• --no-recursion — disable recursive anchor search

🌈 EXAMPLES 🌈

like this, bestie:

progressiveMauve --output=my_seqs.xmfa my_genome1.gbk my_genome2.gbk my_genome3.fasta

if genomes are in a single file and have no rearrangement:

progressiveMauve --collinear --output=my_seqs.xmfa my_genomes.fasta

lowkey the move is: three genomes, one output file, my_seqs.xmfa, and you're the main character of comparative genomics. go off 👑

and that's the whole page, fr fr 💜 this was progressiveMauve 1.2.0+4713, dated April 2015 — yes she's an elder but she ATE and she's still serving. mwah, bye bestie 💅🎀