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LAST-TRAIN(1) User Commands LAST-TRAIN(1)


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.


show this help message and exit
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: 20000 if --codon else 500)
length of each sample (default: 2000)
output scores in units of 1/S bits
DNA queries & protein reference, with frameshifts
Initial parameter options:
match score (default: 6 if Q>=1, or 5 if DNA, or 12)
mismatch cost (default: 18 if Q>=1, or 5 if DNA, or 7)
match/mismatch score matrix
gap existence cost (default: 21 if Q>=1, else 15)
gap extension cost (default: 9 if Q>=1, else 3)
insertion existence cost
insertion extension cost
frameshift probabilities: del-1,del-2,ins+1,ins+2 (default: 1-b,1-b,1-B,1-B)
Alignment options:
query letters per random alignment (default: 1e6)
maximum expected alignments per square giga
0=reverse, 1=forward, 2=both (default: 2 if DNA, else 1)
score matrix applies to forward strand of: 0=reference, 1=query (default: 1)
omit gapless alignments in COUNT others with > scoreper-length
type of alignment: 0=local, 1=overlap (default: 0)
lowercase & simple-sequence options
maximum initial matches per query position (default: 10)
use initial matches starting at every STEP-th position in each query (default: 1)
number of parallel threads
N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (default=0)
input format: fastx, sanger (default=fasta)
January 2023 last-train 1420