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       lastal - genome-scale comparison of biological sequences


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


       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,  Q>0:   6)  -q:  mismatch  cost  (DNA:  1,  protein:
       blosum62,  Q>0:  18) -p: file for residue pair scores -a: gap existence
       cost (DNA: 7, protein: 11, Q>0: 21) -b: gap  extension  cost  (DNA:  1,
       protein:   2,  Q>0:   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, Q>0: 180)

       Miscellaneous  options  (default  settings): -Q: input format: 0=FASTA,
       1=FASTQ-Sanger, 2=FASTQ-Solexa, 3=PRB (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  (16  MiB  if  j=0,  else  1 MiB if Q>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)


       Report bugs to: last (ATmark) cbrc (dot) jp
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