SYNOPSIS

last-train ,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)

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