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LAST-TRAIN(1) User Commands 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
-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
--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: 500)
--sample-length=L
length of each sample (default: 2000)
--scale=S
output scores in units of 1/S bits
Initial parameter options:
-r SCORE
match score (default: 6 if Q>=1, else 5)
-q COST
mismatch cost (default: 18 if Q>=1, else 5)
-p NAME
match/mismatch score matrix
-a COST
gap existence cost (default: 21 if Q>=1, else 15)
-b COST
gap extension cost (default: 9 if Q>=1, 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)
-C COUNT
omit gapless alignments in COUNT others with > scoreper-length
-T NUMBER
type of alignment: 0=local, 1=overlap (default: 0)
-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)
December 2020 last-train 1169