NAME

       lastal5 - genome-scale comparison of biological sequences

SYNOPSIS

       lastal5-plain [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 1<=Q<=4,  else  1  if  DNA)  -q:
       mismatch  cost  (3  if  -M,  else  18  if  1<=Q<=4,  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, 1<=Q<=4: 21) -b: gap extension cost
       (DNA: 1, protein:  2, 1<=Q<=4:  9) -A: insertion existence cost (a) -B: insertion extension cost (b)  -c:
       unaligned  residue  pair  cost  (off) -F: frameshift cost(s) (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: lowercase & simple-sequence options
       (the same as was used by lastdb) -u: mask lowercase during extensions: 0=never, 1=gapless,

              2=gapless+postmask, 3=always (2 if lastdb -c and Q!=pssm, 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)

       -J: score type: 0=ordinary, 1=full (1 for new-style frameshifts, else 0) -Q: input format:  fastx,  keep,
       sanger, solexa, illumina, prb, pssm

              (default=fasta)

lastal5 1260                                      February 2022                                       LASTAL5(1)