---
name: "dawg"
section: "1"
platform: "linux"
package: "dawg"
version: "1.2-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dawg"
---

# dawg(1)

DNA assembly with gaps, a DNA sequence simulator

## 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.