Provided by: last-align_983-1ubuntu2_amd64 bug


       last-train - Try to find suitable score parameters for aligning the given sequences


       last-train [options] lastdb-name sequence-file(s)


       Try to find suitable score parameters for aligning the given sequences.


       -h, --help
              show this help message and exit

       -v, --verbose
              show more details of intermediate steps

              Training options:

              force reverse-complement symmetry

              force symmetric substitution matrix

              force insertion/deletion symmetry

              skip alignments with > PID% identity (default: 100)

              skip mostly-lowercase alignments (default=1)

              number of random sequence samples (default: 500)

              length of each sample (default: 2000)

              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)

       -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 NUMBER
              input format: 0=fasta or fastq-ignore, 1=fastq-sanger (default=fasta)