NAME

       lastal8 - genome-scale comparison of biological sequences

SYNOPSIS

       lastal8-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/