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