NAME

       lastz - pairwise aligning DNA sequences

       lastz_D - pairwise aligning DNA sequences with double-float scoring

DESCRIPTION

       LASTZ  is  a  drop-in  replacement  for  BLASTZ,  and is backward compatible with BLASTZ’s
       command-line syntax. That is, it supports all of BLASTZ’s options but also has  additional
       ones, and may produce slightly different alignment results.

OPTIONS

       target[[start..end]]
              spec/file   containing   target   sequence   (fasta,  fastq,  nib,  2bit  or  hsx);
              [start..end] defines a subrange of the file (use --help=files for more details)

       query[[start..end]]
              spec/file containing query sequences;  if  absent,  queries  come  from  stdin  (if
              needed)

       --self the target sequence is also the query (this replaces the query file)

       --seed=match<length>
              use a word with no gaps instead of a seed pattern

       --[no]transition[=2]
              allow one or two transitions in a seed hit (by default a transition is allowed)

       --step=<length>
              set step length (default is 1)

       --strand=both
              search both strands

       --strand=plus
              search + strand only (matching strand of query spec)

       --strand=minus
              search  -  strand only (opposite strand of query spec) (by default both strands are
              searched)

       --ambiguous=n[,<penalty>] treat N as an ambiguous nucleotide
              (by default N is treated as a sequence splicing

              character)

       --ambiguous=iupac[,<penalty>] treat any ambiguous IUPAC-IUB character as a
              completely   ambiguous   nucleotide   (by   default   any   sequence   file    with
              B,D,H,K,M,R,S,V,W,Y

              is rejected)

       --[no]gfextend
              perform gap-free extension of seed hits to HSPs (by default extension is performed)

       --[no]chain
              perform chaining

       --chain=<diag,anti>
              perform chaining with given penalties for diagonal and anti-diagonal (by default no
              chaining is performed)

       --[no]gapped
              perform gapped alignment (instead of gap-free)  (by  default  gapped  alignment  is
              performed)

       --notrivial
              do  not  output a trivial self-alignment block if the target and query happen to be
              identical

       --scores=<file>
              read substitution scores from a file (default is HOXD70)

       --match=<R>,<P>
              scores are +R/-P for match/mismatch

       --gap=<open,extend>
              set gap open and extend penalties (default is 400,30)

       --xdrop=<score>
              set x-drop threshold (default is 10*sub[A][A])

       --ydrop=<score>
              set y-drop threshold (default is open+300extend)

       --noxtrim
              if x-drop extension encounters end of sequence, don't trim back to peak score  (use
              this for short reads)

       --noytrim
              if  y-drop extension encounters end of sequence, don't trim back to peak score (use
              this for short reads)

       --hspthresh=<score>
              set threshold for high scoring pairs (default is 3000) ungapped extensions  scoring
              lower are discarded <score> can also be a percentage or base count

       --exact=<length>
              set  threshold  for exact matches if specified, exact matches are found rather than
              high scoring pairs (replaces --hspthresh)

       --inner=<score>
              set threshold for HSPs during interpolation (default is no interpolation)

       --gappedthresh=<score> set threshold for gapped alignments
              gapped extensions scoring lower are discarded <score> can also be a  percentage  or
              base count (default is to use same value as --hspthresh)

       --[no]entropy
              involve entropy in filtering high scoring pairs (default is "entropy")

       --nomirror
              don't  report  mirror-image  alignments  when  using  --self  (default  is  to skip
              processing them, but recreate them in the output)

       --allocate:traceback=<bytes>
              space for trace-back information (default is 80.0M)

       --masking=<count>
              mask any position in target hit this many times zero indicates no masking  (default
              is no masking)

       --identity=<min>[..<max>] filter alignments by percent identity
              0<=min<=max<=100;   blocks  (or HSPs) outside min..max are discarded (default is no
              identity filtering)

       --coverage=<min>[..<max>] filter alignments by percentage of query covered
              0<=min<=max<=100;  blocks (or HSPs) outside min..max are discarded (default  is  no
              query coverage filtering)

       --output=<file>
              specify output alignment file;  otherwise alignments are written to stdout

       --format=<type>
              specify  output format; one of lav, axt, maf, cigar, rdotplot, text or general (use
              --help=formats for more details) (by default output is LAV)

       --rdotplot=<file>
              create an output file suitable for plotting in R.

       --progress=<n>
              report processing of every nth query

       --version
              report the program version and quit

       --help list all options

       --help=files
              list information about file specifiers

       --help=formats
              list information about output file formats

       --help=shortcuts
              list blastz-compatible shortcuts

       --help=defaults
              list scoring defaults for your current settings

       --help=yasra
              list yasra-specific shortcuts

SEE ALSO

       The preceding list is not  comprehensive.   The  most  up-to-date  list  is  available  at
       http://www.bx.psu.edu/~rsharris/lastz

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.