-v

be verbose: write messages about what lastal is doing

-2

paired query sequences

-f

output format: TAB, MAF, BlastTab, BlastTab+ (default: MAF)

-D

query letters per random alignment (default: 1e+06)

-H

expected total number of random alignments for all the sequences

-E

max EG2: expected number of random alignments per square giga

-r

match score (2 if -M , else 1)

-q

mismatch cost (3 if -M , else 1)

-p

match/mismatch score matrix (DNA-DNA: HUMSUM, protein-protein: BLOSUM62, DNA-protein: BLOSUM80)

-X

N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (0)

-a

gap existence cost (24 if HUMSUM, else 11 if protein reference, else 7)

-b

gap extension cost ( 1 if HUMSUM, else 2 if protein reference, else 1)

-A

insertion existence cost (a)

-B

insertion extension cost (b)

-c

unaligned residue pair cost (off)

-F

frameshift cost(s) (off)

-x

maximum score drop for preliminary gapped alignments (z)

-y

maximum score drop for gapless alignments (min[t*10, x])

-z

maximum score drop for final gapped alignments (e-1)

-d

minimum score for gapless alignments (min[e, 2500/n query letters per hit])

-e

minimum score for gapped alignments

-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

-P

number of parallel threads (default: 1)

-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)

-s

strand: 0=reverse, 1=forward, 2=both (2 if DNA and not lastdb -S2 , else 1)

-S

use score matrix: 0=as-is, 1=on query forward strands (0)

-i

query batch size (64M if multi-volume, else off)

-M

find minimum-difference alignments (faster but cruder)

-T

type of alignment: 0=local, 1=overlap (default: 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

lowercase & simple-sequence options (the same as was used by lastdb)

-U

maximum tandem repeat unit length (100 if --codon else same as lastdb)

-u

mask lowercase during extensions: 0=never, 1=gapless, 2=gapless+postmask, 3=always (2 if lastdb -c and Q!=pssm, else 0)

-w

suppress repeats inside exact matches, offset by <= this distance (1000)

-G

genetic code (default: 1)

-t

’temperature’ for calculating probabilities (1/lambda)

-g

’gamma’ parameter for gamma-centroid and LAMA (default: 1)

-j

output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped,

-J

score type: 0=ordinary, 1=full (1 for new-style frameshifts, else 0)

-Q

input format: fastx, keep, sanger, solexa, illumina, prb, pssm