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last-train - Online in the Cloud

Run last-train in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command last-train that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


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

SYNOPSIS


last-train 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

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)

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)

-T NUMBER
type of alignment: 0=local, 1=overlap (default: 0)

-m COUNT
maximum initial matches per query position (default: 10)

-P THREADS
number of parallel threads

-Q NUMBER
input format: 0=fasta, 1=fastq-sanger

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