---
name: "progressiveMauve"
section: "1"
platform: "linux"
package: "progressivemauve"
version: "1.2.0+4713+dfsg-5+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/progressiveMauve"
---

# progressiveMauve(1)

efficiently constructing multiple genome alignments

## NAME

progressiveMauve - efficiently constructing multiple genome alignments

## DESCRIPTION

progressiveMauve usage:

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\>

## OPTIONS

**--island-gap-size=**\<number\> Alignment gaps above this size in nucleotides are considered to be islands \[20\]

**--profile=**\<file\> (Not yet implemented) Read an existing sequence alignment in XMFA format and align it to other sequences or alignments

**--apply-backbone=**\<file\> Read an existing sequence alignment in XMFA format and apply backbone statistics to it

**--disable-backbone** Disable backbone detection

**--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)

- **--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.

**--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

**--no-recursion** Disable recursive anchor search

## EXAMPLES

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