---
name: "lastal"
section: "1"
platform: "linux"
package: "last-align"
version: "1609-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/lastal"
---

# lastal(1)

genome-scale comparison of biological sequences

## NAME

lastal - genome-scale comparison of biological sequences

## SYNOPSIS

**lastal-plain** \[*options*\] *lastdb-name fasta-sequence-file(s)*

## DESCRIPTION

Find and align similar sequences.

### Cosmetic options:

- **-h**, **--help**

  show all options and their default settings, and exit

- **-V**, **--version**

  show version information, and exit

- **-v**

  be verbose: write messages about what lastal is doing

- **-2**

  paired query sequences

- **-f**

  output format: TAB, MAF, BlastTab, BlastTab+ (default: MAF)

### E-value options (default settings):

- **-D**

  query letters per random alignment (default: 1e+06)

- **-H**

  expected total number of random alignments for all the sequences

- **-E**

  max EG2: expected number of random alignments per square giga

### Score options (default settings):

- **-r**

  match score   (2 if **-M**, else 1)

- **-q**

  mismatch cost (3 if **-M**, else 1)

- **-p**

  match/mismatch score matrix (DNA-DNA: HUMSUM, protein-protein: BLOSUM62, DNA-protein: BLOSUM80)

- **-X**

  N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (0)

- **-a**

  gap existence cost (24 if HUMSUM, else 11 if protein reference, else 7)

- **-b**

  gap extension cost ( 1 if HUMSUM, else  2 if protein reference, else 1)

- **-A**

  insertion existence cost (a)

- **-B**

  insertion extension cost (b)

- **-c**

  unaligned residue pair cost (off)

- **-F**

  frameshift cost(s) (off)

- **-x**

  maximum score drop for preliminary gapped alignments (z)

- **-y**

  maximum score drop for gapless alignments (min\[t\*10, x\])

- **-z**

  maximum score drop for final gapped alignments (e-1)

- **-d**

  minimum score for gapless alignments (min\[e, 2500/n query letters per hit\])

- **-e**

  minimum score for gapped alignments

### Initial-match options (default settings):

- **-m**

  maximum initial matches per query position (10)

- **-l**

  minimum length for initial matches (1)

- **-L**

  maximum length for initial matches (infinity)

- **-k**

  use initial matches starting at every k-th position in each query (1)

- **-W**

  use "minimum" positions in sliding windows of W consecutive positions

### Miscellaneous options (default settings):

- **-P**

  number of parallel threads (default: 1)

- **-K**

  omit alignments whose query range lies in \>= K others with \> score (off)

- **-C**

  omit gapless alignments in \>= C others with \> score-per-length (off)

- **-s**

  strand: 0=reverse, 1=forward, 2=both (2 if DNA and not lastdb **-S2**, else 1)

- **--reverse**

  reverse the query sequences

- **-S**

  use score matrix: 0=as-is, 1=on query forward strands (0)

- **-i**

  query batch size (64M if multi-volume, else off)

- **-M**

  find minimum-difference alignments (faster but cruder)

- **-T**

  type of alignment: 0=local, 1=overlap (default: 0)

- **-n**

  maximum gapless alignments per query position (infinity if m=0, else m)

- **-N**

  stop after the first N alignments per query strand

- **-R**

  lowercase & simple-sequence options (the same as was used by lastdb)

- **-U**

  maximum tandem repeat unit length (100 if **--codon** else same as lastdb)

- **-u**

  mask lowercase during extensions: 0=never, 1=gapless, 2=gapless+postmask, 3=always (2 if lastdb **-c** and Q!=pssm, else 0)

- **-w**

  suppress repeats inside exact matches, offset by \<= this distance (1000)

- **-G**

  genetic code (default: 1)

- **-t**

  'temperature' for calculating probabilities (1/lambda)

- **-g**

  'gamma' parameter for gamma-centroid and LAMA (default: 1)

- **-j**

  output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped,

-

  4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA, 7=expected counts (default: 3)

- **-J**

  score type: 0=ordinary, 1=full (1 for new-style frameshifts, else 0)

- **-Q**

  input format: fastx, keep, sanger, solexa, illumina, prb, pssm

-

  (default: fasta)

### Split options:

- **--split**

  do split alignment

- **--splice**

  do spliced alignment

- **--split-f**=*FMT*

  output format: MAF, MAF+

- **--split-d**=*D*

  RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1)

- **--split-c**=*PROB*

  cis-splice probability per base (default: 0.004)

- **--split-t**=*PROB*

  trans-splice probability per base (default: 1e-05)

- **--split-M**=*MEAN*

  mean of ln\[intron length\] (default: 7.0)

- **--split-S**=*SDEV*

  standard deviation of ln\[intron length\] (default: 1.7)

- **--split-m**=*PROB*

  maximum mismap probability (default: 1.0)

- **--split-s**=*INT*

  minimum alignment score (default: e OR e+t\*ln\[100\])

- **--split-n**

  write original, not split, alignments

- **--split-b**=*B*

  maximum memory (default: 8T for split, 8G for spliced)