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] -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.*
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.
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