NAME

       lastal8 - genome-scale comparison of biological sequences

SYNOPSIS

       lastal8 [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) -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 gapped alignments (e-1) -y: maximum
       score drop for gapless alignments (min[t*10, x]) -z: maximum score drop for  final  gapped
       alignments (x) -d: minimum score for gapless alignments (min[e, t*ln(1000*refSize/n)]) -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 file -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, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,

              4=prb, 5=PSSM (0)

REPORTING BUGS

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