NAME
last-train - Try to find suitable score parameters for aligning the given sequences
SYNOPSIS
last-train [options] lastdb-name sequence-file(s)
DESCRIPTION
Try to find suitable score parameters for aligning the given sequences.
OPTIONS
- -h, --help
-
show this help message and exit
- -v, --verbose
-
show more details of intermediate steps
-
Training options:
- --revsym
-
force reverse-complement symmetry
- --matsym
-
force symmetric substitution matrix
- --gapsym
-
force insertion/deletion symmetry
- --fixmat=NAME
-
fix the substitution probabilities to e.g. BLOSUM62
- --pid=PID
-
skip alignments with > PID% identity (default: 100)
- --postmask=NUMBER
-
skip mostly-lowercase alignments (default=1)
- --sample-number=N
-
number of random sequence samples (default: 20000 if --codon else 500)
- --sample-length=L
-
length of each sample (default: 2000)
- --scale=S
-
output scores in units of 1/S bits
- --codon
-
DNA queries & protein reference, with frameshifts
-
Initial parameter options:
- -r SCORE
-
match score
- -q COST
-
mismatch cost
- -p NAME
-
match/mismatch score matrix
- -a COST
-
gap existence cost
- -b COST
-
gap extension cost
- -A COST
-
insertion existence cost
- -B COST
-
insertion extension cost
- -F LIST
-
frameshift probabilities: del-1,del-2,ins+1,ins+2 (default: 1-b,1-b,1-B,1-B)
-
Alignment options:
- -D LENGTH
-
query letters per random alignment (default: total sample length)
- -E EG2
-
maximum expected alignments per square giga
- -s STRAND
-
0=reverse, 1=forward, 2=both (default: 2 if DNA and not lastdb -S2, else 1)
- -S NUMBER
-
use score matrix: 0=as-is, 1=on query forward strands (default: 1)
- -C COUNT
-
omit gapless alignments in COUNT others with > scoreper-length
- -T NUMBER
-
type of alignment: 0=local, 1=overlap (default: 0)
- -R DIGITS
-
lowercase & simple-sequence options
- -m COUNT
-
maximum initial matches per query position (default: 10)
- -k STEP
-
use initial matches starting at every STEP-th position in each query (default: 1)
- -P THREADS
-
number of parallel threads
- -X NUMBER
-
N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (default=0)
- -Q NAME
-
input format: fastx, sanger (default=fasta)