DAWG

NAME

dawg - DNA assembly with gaps, a DNA sequence simulator

DESCRIPTION

dawg 1.2-release DNA Assembly With Gaps Copyright © 2004-2009 Reed A. Cartwright

dawg -[scubvhqew?] [-o outputfile] file1 [file2...]

	-s: process files serially [default]
	-c: process files combined together
	-u: unbuffered output
	-b: buffered output [default]
	-q: disable error and warning reports (quiet)
	-e: enable error reports [default]
	-w: enable warning reports [default]
	-v: display version information
	-h: display help information
	-?: same as -h
	-o outputfile: override output filename in the configuration file

Dawg will read stdin if filename is "-".

FILE FORMAT

The file format takes a series of statements in the form of "name = value," where "name" is alphanumeric and value can be a string, number, boolean, tree, or vector of values. A single variable is equivalent to a vector of a single entry.

string: "[char-sequence]"

’[char-sequence]’ """[multi-line char-sequence]""" (rm initial and final newlines) ’’’[multi-line char-sequence]’’’ (kp initial and final newlines)

number: [sign]digits[.digits][(e|E)[sign]digits] boolean: true|false tree: Newick Format vector: { value, value, ...}

OPTIONS

	Name
			Type Description

---------------------------------

Tree

VT phylogeny

TreeScale

N coefficient to scale branch lengths by

Sequence

VS root sequences

Length

VN length of generated root sequences

	Rates		VVN rate of evolution of each root nucleotide
	Model		S model of evolution: GTR|JC|K2P|K3P|HKY|F81|F84|TN
	Freqs		VN nucleotide (ACGT) frequencies

Params

VN parameters for the model of evolution

	Width		N block width for indels and recombination
	Scale		VN block position scales
	Gamma		VN coefficients of variance for rate heterogenity
	Alpha		VN shape parameters
	Iota		VN proportions of invariant sites

GapModel

VS models of indel formation: NB|PL|US

Lambda

VN rates of indel formation

GapParams

VVN parameter for the indel model

	Reps		N number of data sets to output
	File		S output file

Format

S output format: Fasta|Nexus|Phylip|Clustal

GapSingleChar

B output gaps as a single character

GapPlus

B distinguish insertions from deletions in alignment

KeepFlank

N undeletable flanking regions N nucs from sequence

KeepEmpty

B preserve empty columns in final alignment

LowerCase

B output sequences in lowercase

Translate

B translate outputed sequences to amino acids

Seed

VN pseudo-random-number-generator seed (integers)

Out.Block.Head

S string to insert at the start of the output

Out.Block.Tail

S string to insert at the end of the output

Out.Block.Before S

string to insert before a sequence set in the output

Out.Block.After

S string to insert after a sequence set in the output

Out.Subst

B do variable subsitution in Out.Block.*

LICENSE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

Send Bug Reports to reed@scit.us.