last-train(1)
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
Training options:
--revsym
force reverse-complement symmetry
--matsym
force symmetric substitution matrix
--gapsym
force insertion/deletion symmetry
--pid=PID
skip alignments with > PID% identity (default: 100)
--sample=N
use a random sample of N letters (default: 1000000)
Initial parameter options:
-r SCORE
match score (default: 6 if Q>0, else 5)
-q COST
mismatch cost (default: 18 if Q>0, else 5)
-p NAME
match/mismatch score matrix
-a COST
gap existence cost (default: 21 if Q>0, else 15)
-b COST
gap extension cost (default: 9 if Q>0, else 3)
-A COST
insertion existence cost
-B COST
insertion extension cost
Alignment options:
-D LENGTH
query letters per random alignment (default: 1e6)
-E EG2 maximum expected alignments per square giga
-s STRAND
0=reverse, 1=forward, 2=both (default: 2 if DNA, else 1)
-S NUMBER
score matrix applies to forward strand of: 0=reference, 1=query
(default: 1)
-T NUMBER
type of alignment: 0=local, 1=overlap (default: 0)
-m COUNT
maximum initial matches per query position (default: 10)
-P THREADS
number of parallel threads
-Q NUMBER
input format: 0=fasta, 1=fastq-sanger
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