---
name: "last-train"
section: "1"
platform: "linux"
package: "last-align"
version: "1609-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/last-train"
---

# last-train(1)

Try to find suitable score parameters for aligning the given sequences

## 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)