NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

       lastal [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/

lastal 921                                        February 2018                                        LASTAL(1)