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:
- --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: 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 (default: 6 if Q>=1, or 5 if DNA, or 12)
- -q COST
- mismatch cost (default: 18 if Q>=1, or 5 if DNA, or 7)
- -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
- -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: 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)
- -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)