lastal - genome-scale comparison of biological sequences
lastal-plain [options] lastdb-name
fasta-sequence-file(s)
Find and align similar sequences.
- -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
- -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)
- --reverse
- reverse the query sequences
- -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,
- 4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA, 7=expected counts
(default: 3)
- -J
- score type: 0=ordinary, 1=full (1 for new-style frameshifts, else 0)
- -Q
- input format: fastx, keep, sanger, solexa, illumina, prb, pssm
- (default: fasta)