.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH PROGRESSIVEMAUVE "1" "April 2015" "progressiveMauve 1.2.0+4713" "User Commands"
.SH NAME
progressiveMauve \- efficiently constructing multiple genome alignments
.SH DESCRIPTION
progressiveMauve usage:
.PP
When each genome resides in a separate file:
progressiveMauve [options] <seq1 filename> ... <seqN filename>
.PP
When all genomes are in a single file:
progressiveMauve [options] <seq filename>
.SH OPTIONS
.HP
\fB\-\-island\-gap\-size=\fR<number> Alignment gaps above this size in nucleotides are considered to be islands [20]
.HP
\fB\-\-profile=\fR<file> (Not yet implemented) Read an existing sequence alignment in XMFA format and align it to other sequences or alignments
.HP
\fB\-\-apply\-backbone=\fR<file> Read an existing sequence alignment in XMFA format and apply backbone statistics to it
.HP
\fB\-\-disable\-backbone\fR Disable backbone detection
.HP
\fB\-\-mums\fR Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)
.HP
\fB\-\-seed\-weight=\fR<number> Use the specified seed weight for calculating initial anchors
.TP
\fB\-\-output=\fR<file> Output file name.
Prints to screen by default
.HP
\fB\-\-backbone\-output=\fR<file> Backbone output file name (optional).
.HP
\fB\-\-match\-input=\fR<file> Use specified match file instead of searching for matches
.HP
\fB\-\-input\-id\-matrix=\fR<file> An identity matrix describing similarity among all pairs of input sequences/alignments
.HP
\fB\-\-max\-gapped\-aligner\-length=\fR<number> Maximum number of base pairs to attempt aligning with the gapped aligner
.HP
\fB\-\-input\-guide\-tree=\fR<file> A phylogenetic guide tree in NEWICK format that describes the order in which sequences will be aligned
.HP
\fB\-\-output\-guide\-tree=\fR<file> Write out the guide tree used for alignment to a file
.HP
\fB\-\-version\fR Display software version information
.HP
\fB\-\-debug\fR Run in debug mode (perform internal consistency checks\-\-very slow)
.TP
\fB\-\-scratch\-path\-1=\fR<path> Designate a path that can be used for temporary data storage.
Two or more paths should be specified.
.TP
\fB\-\-scratch\-path\-2=\fR<path> Designate a path that can be used for temporary data storage.
Two or more paths should be specified.
.HP
\fB\-\-collinear\fR Assume that input sequences are collinear\-\-they have no rearrangements
.TP
\fB\-\-scoring\-scheme=\fR<ancestral|sp_ancestral|sp> Selects the anchoring score function.
Default is extant sum\-of\-pairs (sp).
.HP
\fB\-\-no\-weight\-scaling\fR Don't scale LCB weights by conservation distance and breakpoint distance
.TP
\fB\-\-max\-breakpoint\-distance\-scale=\fR<number [0,1]> Set the maximum weight scaling by breakpoint distance.
Defaults to 0.5
.TP
\fB\-\-conservation\-distance\-scale=\fR<number [0,1]> Scale conservation distances by this amount.
Defaults to 0.5
.TP
\fB\-\-muscle\-args=\fR<arguments in quotes> Additional command\-line options for MUSCLE.
Any quotes should be escaped with a backslash
.HP
\fB\-\-skip\-refinement\fR Do not perform iterative refinement
.HP
\fB\-\-skip\-gapped\-alignment\fR Do not perform gapped alignment
.HP
\fB\-\-bp\-dist\-estimate\-min\-score=\fR<number> Minimum LCB score for estimating pairwise breakpoint distance
.HP
\fB\-\-mem\-clean\fR Set this to true when debugging memory allocations
.HP
\fB\-\-gap\-open=\fR<number> Gap open penalty
.TP
\fB\-\-repeat\-penalty=\fR<negative|zero> Sets whether the repeat scores go negative or go to zero for highly repetitive sequences.
Default is negative.
.HP
\fB\-\-gap\-extend=\fR<number> Gap extend penalty
.HP
\fB\-\-substitution\-matrix=\fR<file> Nucleotide substitution matrix in NCBI format
.HP
\fB\-\-weight=\fR<number> Minimum pairwise LCB score
.HP
\fB\-\-min\-scaled\-penalty=\fR<number> Minimum breakpoint penalty after scaling the penalty by expected divergence
.HP
\fB\-\-hmm\-p\-go\-homologous=\fR<number> Probability of transitioning from the unrelated to the homologous state [0.00001]
.HP
\fB\-\-hmm\-p\-go\-unrelated=\fR<number> Probability of transitioning from the homologous to the unrelated state [0.000000001]
.HP
\fB\-\-hmm\-identity=\fR<number> Expected level of sequence identity among pairs of sequences, ranging between 0 and 1 [0.7]
.HP
\fB\-\-seed\-family\fR Use a family of spaced seeds to improve sensitivity
.HP
\fB\-\-solid\-seeds\fR Use solid seeds. Do not permit substitutions in anchor matches.
.HP
\fB\-\-coding\-seeds\fR Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy.
.HP
\fB\-\-disable\-cache\fR Disable recursive anchor search cacheing to workaround a crash bug
.HP
\fB\-\-no\-recursion\fR Disable recursive anchor search
.SH EXAMPLES
progressiveMauve \-\-output=my_seqs.xmfa my_genome1.gbk my_genome2.gbk my_genome3.fasta
.PP
If genomes are in a single file and have no rearrangement:
progressiveMauve \-\-collinear \-\-output=my_seqs.xmfa my_genomes.fasta