dawg − DNA assembly with gaps, a DNA sequence simulator
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] |
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−c: process files combined together |
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−u: unbuffered output |
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−b: buffered output [default] |
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−q: disable error and warning reports (quiet) |
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−e: enable error reports [default] |
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−w: enable warning reports [default] |
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−v: display version information |
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−h: display help information |
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−?: same as −h |
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−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 |
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Type Description |
−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
Tree |
VT phylogeny |
TreeScale
N coefficient to scale branch lengths by
Sequence
VS root sequences
Length |
VN length of generated root sequences |
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Rates |
VVN rate of evolution of each root nucleotide |
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Model |
S model of evolution: GTR|JC|K2P|K3P|HKY|F81|F84|TN |
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Freqs |
VN nucleotide (ACGT) frequencies |
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Params |
VN parameters for the model of evolution |
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Width |
N block width for indels and recombination |
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Scale |
VN block position scales |
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Gamma |
VN coefficients of variance for rate heterogenity |
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Alpha |
VN shape parameters |
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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 |
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File |
S output file |
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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.*
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 AT scit DOT us.