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 [email protected].