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DAWG(1) User Commands DAWG(1)

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

Type Description

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

VT phylogeny
N coefficient to scale branch lengths by
VS root sequences
VN length of generated root sequences
VVN rate of evolution of each root nucleotide
S model of evolution: GTR|JC|K2P|K3P|HKY|F81|F84|TN
VN nucleotide (ACGT) frequencies
VN parameters for the model of evolution
N block width for indels and recombination
VN block position scales
VN coefficients of variance for rate heterogenity
VN shape parameters
VN proportions of invariant sites
VS models of indel formation: NB|PL|US
VN rates of indel formation
VVN parameter for the indel model
N number of data sets to output
S output file
S output format: Fasta|Nexus|Phylip|Clustal
B output gaps as a single character
B distinguish insertions from deletions in alignment
N undeletable flanking regions N nucs from sequence
B preserve empty columns in final alignment
B output sequences in lowercase
B translate outputed sequences to amino acids
VN pseudo-random-number-generator seed (integers)
S string to insert at the start of the output
S string to insert at the end of the output
string to insert before a sequence set in the output
S string to insert after a sequence set in the output
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.

December 2015 dawg 1.2-release