---
name: "lastal8"
section: "1"
platform: "linux"
package: "last-align"
version: "1179-1+b1"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/lastal8"
---

# lastal8(1)

genome-scale comparison of biological sequences

## NAME

lastal8 - genome-scale comparison of biological sequences

## SYNOPSIS

**lastal8-avx2** \[*options*\] *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 **-f**: output format: TAB, MAF, BlastTab, BlastTab+ (default=MAF)

E-value options (default settings): **-D**: query letters per random alignment (1e+06) **-E**: maximum expected alignments per square giga (1e+18/D/refSize/numOfStrands)

Score options (default settings): **-r**: match score   (2 if **-M**, else  6 if 1\<=Q\<=4, else 1 if DNA) **-q**: mismatch cost (3 if **-M**, else 18 if 1\<=Q\<=4, else 1 if DNA) **-p**: match/mismatch score matrix (protein-protein: BL62, DNA-protein: BL80) **-X**: N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (0) **-a**: gap existence cost (DNA: 7, protein: 11, 1\<=Q\<=4: 21) **-b**: gap extension cost (DNA: 1, protein:  2, 1\<=Q\<=4:  9) **-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): **-s**: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) **-S**: score matrix applies to forward strand of: 0=reference, 1=query (0) **-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) **-P**: number of parallel threads (1) **-i**: query batch size (8 KiB, unless there is \> 1 thread or lastdb volume) **-M**: find minimum-difference alignments (faster but cruder) **-T**: type of alignment: 0=local, 1=overlap (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**: repeat-marking options (the same as was used for 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 (1) **-t**: 'temperature' for calculating probabilities (1/lambda) **-g**: 'gamma' parameter for gamma-centroid and LAMA (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 (3)

**-Q**: input format: fastx, keep, sanger, solexa, illumina, prb, pssm

-

  (default=fasta)

## REPORTING BUGS

Report bugs to: last-align (ATmark) googlegroups (dot) com\
 LAST home page: http://last.cbrc.jp/