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lastal - genome-scale comparison of biological sequences


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


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)


Report bugs to: last-align (ATmark) googlegroups (dot) com
LAST home page: http://last.cbrc.jp/

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