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)