xenial (1) lastal.1.gz

Provided by: last-align_712-1ubuntu1_amd64 bug

NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

       lastal [options] lastdb-name fasta-sequence-file(s)

DESCRIPTION

       Find local sequence alignments.

       Score options (default settings): -r: match score   (DNA: 1, 0<Q<5:  6) -q: mismatch cost (DNA: 1, 0<Q<5:
       18) -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 (max[y, e-1]) -y: maximum score drop for gapless
       alignments (t*10) -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

       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)

       Cosmetic options (default settings): -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 (MAF)

       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) -T: type of alignment:
       0=local, 1=overlap (0) -m: maximum initial matches per query position (10) -l: minimum length for initial
       matches  (1)  -L:  maximum length for initial matches (infinity) -n: maximum gapless alignments per query
       position (infinity if m=0, else m) -C: omit gapless alignments in >= C  others  with  >  score-per-length
       (off)  -K:  omit  alignments whose query range lies in >= K others with > score (off) -k: step-size along
       the query sequence (1) -i: query batch size (8 KiB, unless there is > 1  thread  or  lastdb  volume)  -P:
       number  of  parallel  threads  (1)  -R: repeat-marking options (the same as was used for lastdb) -u: mask
       lowercase during extensions: 0=never, 1=gapless,

              2=gapless+gapped but not final, 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/