LASTAL(1)
NAME
lastal - genome-scale comparison of biological sequences
SYNOPSIS
lastal [options] lastdb-name fasta-sequence-file(s)
DESCRIPTION
Find local sequence alignments.
Main options (default settings): -h: show all options and their default
settings -o: output file -s: strand: 0=reverse, 1=forward, 2=both (2
for DNA, 1 for protein) -f: output format: 0=tabular, 1=maf (1)
Score parameters (default settings): -r: match score (DNA: 1, protein: blosum62, 0<Q<4: 6) -q: mismatch cost (DNA: 1, protein: blosum62, 0<Q<4: 18) -p: file for residue pair scores -a: gap existence
cost (DNA: 7, protein: 11, 0<Q<4: 21) -b: gap extension cost (DNA: 1,
protein: 2, 0<Q<4: 9) -c: unaligned residue pair cost (100000) -F:
frameshift cost (off) -x: maximum score dropoff for gapped extensions
(max[y, a+b*20]) -y: maximum score dropoff for gapless extensions
(t*10) -d: minimum score for gapless alignments (e*3/5) -e: minimum
score for gapped alignments (DNA: 40, protein: 100, 0<Q<4: 180)
- Miscellaneous options (default settings): -Q: input format: 0=FASTA,
1=FASTQ-Sanger, 2=FASTQ-Solexa, 3=PRB, 4=PSSM (0) -u: mask lowercase
during extensions: 0=neither, 1=gapless, 2=gapless+gapped (0) -m: maximum multiplicity for initial matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query
position (infinity) -k: step-size along the query sequence (1) -i:
query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128 MiB) -w:
supress repeats within this distance inside large exact matches (1000)
-t: 'temperature' for calculating probabilities (1/lambda) -g: 'gamma'
parameter for gamma-centroid alignment (1) -G: genetic code file -v: be
verbose: write messages about what lastal is doing -j: output type:
0=match counts, 1=gapless, 2=redundant gapped, 3=gapped,
- 4=probabilities, 5=centroid (3)
REPORTING BUGS
- Report bugs to: last (ATmark) cbrc (dot) jp
LAST home page: http://last.cbrc.jp/