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