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LASTAL(1) User Commands LASTAL(1)


lastal - genome-scale comparison of biological sequences


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


Find and align similar sequences.

Cosmetic options:

show all options and their default settings, and exit
show version information, and exit
be verbose: write messages about what lastal is doing
output format: TAB, MAF, BlastTab, BlastTab+ (default: MAF)

E-value options (default settings):

query letters per random alignment (1e+06)
maximum expected alignments per square giga (1e+18/D/refSize/numOfStrands)

Score options (default settings):

match score (2 if -M, else 6 if 1<=Q<=4, else 1 if DNA)
mismatch cost (3 if -M, else 18 if 1<=Q<=4, else 1 if DNA)
match/mismatch score matrix (protein-protein: BL62, DNA-protein: BL80)
N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (0)
gap existence cost (DNA: 7, protein: 11, 1<=Q<=4: 21)
gap extension cost (DNA: 1, protein: 2, 1<=Q<=4: 9)
insertion existence cost (a)
insertion extension cost (b)
unaligned residue pair cost (off)
frameshift cost(s) (off)
maximum score drop for preliminary gapped alignments (z)
maximum score drop for gapless alignments (min[t*10, x])
maximum score drop for final gapped alignments (e-1)
minimum score for gapless alignments (min[e, 2500/n query letters per hit])
minimum score for gapped alignments

Initial-match options (default settings):

maximum initial matches per query position (10)
minimum length for initial matches (1)
maximum length for initial matches (infinity)
use initial matches starting at every k-th position in each query (1)
use "minimum" positions in sliding windows of W consecutive positions

Miscellaneous options (default settings):

strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein)
score matrix applies to forward strand of: 0=reference, 1=query (0)
omit alignments whose query range lies in >= K others with > score (off)
omit gapless alignments in >= C others with > score-per-length (off)
number of parallel threads (1)
query batch size (64M if multi-volume, else off)
find minimum-difference alignments (faster but cruder)
type of alignment: 0=local, 1=overlap (0)
maximum gapless alignments per query position (infinity if m=0, else m)
stop after the first N alignments per query strand
lowercase & simple-sequence options (the same as was used by lastdb)
mask lowercase during extensions: 0=never, 1=gapless, 2=gapless+postmask, 3=always (2 if lastdb -c and Q!=pssm, else 0)
suppress repeats inside exact matches, offset by <= this distance (1000)
genetic code (1)
'temperature' for calculating probabilities (1/lambda)
'gamma' parameter for gamma-centroid and LAMA (1)
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)
score type: 0=ordinary, 1=full (1 for new-style frameshifts, else 0)
input format: fastx, keep, sanger, solexa, illumina, prb, pssm
(default: fasta)

Split options:

do split alignment
do spliced alignment
output format: MAF, MAF+
RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1)
cis-splice probability per base (default: 0.004)
trans-splice probability per base (default: 1e-05)
mean of ln[intron length] (default: 7.0)
standard deviation of ln[intron length] (default: 1.7)
maximum mismap probability (default: 1.0)
minimum alignment score (default: e OR e+t*ln[100])
write original, not split, alignments
maximum memory (default: 8T for split, 8G for spliced)
January 2023 lastal 1420