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)

last-train 1609                                   February 2025                                    LAST-TRAIN(1)