hmm-assembler.pl(1)

The following single-character options are accepted:

With arguments: -i -e -A -D -M -S -C -I -N -a -3 -5 -Z -c

Boolean (without arguments): -r -o -x -p -t -1

Options may be merged together. -- stops processing of options. Space is not required between options and their arguments.

Options:

-i

<length> [500]

-e

<length> [1000]

-A

<order:length> [0:30]

-D

<order:length> [0:9]

-M

<order:length> [0:15]

-S

<order:length> [0:9]

-C

<order> [4]

-I

<order> [4]

-N

<order> [4]

-3

<order:length> [] include 3'UTR model, requires -a

-a

<order:length> [] include PolyA model, requires -3

-5

<order:length> [] include 5'UTR moel, requires -p

-p

include generic promoter model, requires -5

-r

include generic repeat model

-o

include reverse ORF model

-x

use explicit duration intron model

-t

include C.elegans trans-splicing, requires -p, -5

-Z

<clade> sets clade-specific values (worm, fly, plant)

-1

single gene model

-c <score>

include GC-AG splice donor model