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 (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
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)
-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/