NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

       lastal-avx [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 0<Q<5, else 1  if
       DNA) -q: mismatch cost (3 if -M, else 18 if 0<Q<5, 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,
       0<Q<5: 21) -b: gap extension cost (DNA: 1, protein:  2, 0<Q<5:  9) -A: insertion existence
       cost  (a)  -B:  insertion  extension  cost  (b)  -c: unaligned residue pair cost (off) -F:
       frameshift cost (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<5, 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: 0=fasta or fastq-ignore, 1=fastq-sanger, 2=fastq-solexa,

              3=fastq-illumina, 4=prb, 5=PSSM (fasta)

REPORTING BUGS

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