.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH LAST-TRAIN "1" "January 2019" "last-train 963" "User Commands"
.SH NAME
last-train \- Try to find suitable score parameters for aligning the given sequences
.SH SYNOPSIS
.B last-train
[\fI\,options\/\fR] \fI\,lastdb-name sequence-file(s)\/\fR
.SH DESCRIPTION
Try to find suitable score parameters for aligning the given sequences.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-v\fR, \fB\-\-verbose\fR
show more details of intermediate steps
.IP
Training options:
.TP
\fB\-\-revsym\fR
force reverse\-complement symmetry
.TP
\fB\-\-matsym\fR
force symmetric substitution matrix
.TP
\fB\-\-gapsym\fR
force insertion/deletion symmetry
.TP
\fB\-\-pid\fR=\fI\,PID\/\fR
skip alignments with > PID% identity (default: 100)
.TP
\fB\-\-postmask\fR=\fI\,NUMBER\/\fR
skip mostly\-lowercase alignments (default=1)
.TP
\fB\-\-sample\-number\fR=\fI\,N\/\fR
number of random sequence samples (default: 500)
.TP
\fB\-\-sample\-length\fR=\fI\,L\/\fR
length of each sample (default: 2000)
.IP
Initial parameter options:
.TP
\fB\-r\fR SCORE
match score (default: 6 if Q>0, else 5)
.TP
\fB\-q\fR COST
mismatch cost (default: 18 if Q>0, else 5)
.TP
\fB\-p\fR NAME
match/mismatch score matrix
.TP
\fB\-a\fR COST
gap existence cost (default: 21 if Q>0, else 15)
.TP
\fB\-b\fR COST
gap extension cost (default: 9 if Q>0, else 3)
.TP
\fB\-A\fR COST
insertion existence cost
.TP
\fB\-B\fR COST
insertion extension cost
.IP
Alignment options:
.TP
\fB\-D\fR LENGTH
query letters per random alignment (default: 1e6)
.TP
\fB\-E\fR EG2
maximum expected alignments per square giga
.TP
\fB\-s\fR STRAND
0=reverse, 1=forward, 2=both (default: 2 if DNA, else
1)
.TP
\fB\-S\fR NUMBER
score matrix applies to forward strand of: 0=reference,
1=query (default: 1)
.TP
\fB\-C\fR COUNT
omit gapless alignments in COUNT others with > scoreper\-length
.TP
\fB\-T\fR NUMBER
type of alignment: 0=local, 1=overlap (default: 0)
.TP
\fB\-m\fR COUNT
maximum initial matches per query position (default:
10)
.TP
\fB\-k\fR STEP
use initial matches starting at every STEP\-th position
in each query (default: 1)
.TP
\fB\-P\fR THREADS
number of parallel threads
.TP
\fB\-Q\fR NUMBER
input format: 0=fasta or fastq\-ignore, 1=fastq\-sanger
(default=fasta)