---
name: "lastz"
section: "1"
platform: "linux"
package: "lastz"
version: "1.04.22-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/lastz"
---

# lastz(1)

pairwise aligning DNA sequences lastz\_D - pairwise aligning DNA sequences with double-float scoring

## 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.