DAWG(1)

🐶 NAME 🐶

dawg — DNA assembly with gaps, a DNA sequence simulator. she's a section 1 page, so it's DAWG(1) when you cite her, bestie. 💅

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✨ DESCRIPTION ✨

okay so. this is dawg 1.2-release, aka DNA Assembly With Gaps, copyright © 2004-2009 Reed A. Cartwright. iconic behavior honestly.

here's the whole invocation vibe:

dawg -[scubvhqew?] [-o outputfile] file1 [file2...]

and here's what every one of those little letters is doing 👇

• -s — process files serially. this is the default, periodt.
• -c — process files combined together.
• -u — unbuffered output.
• -b — buffered output. also the default 💖
• -q — disable error and warning reports (quiet mode, shhh).
• -e — enable error reports. default, she's chatty.
• -w — enable warning reports. default too.
• -v — display version information.
• -h — display help information.
• -? — same as -h. literally the same thing, not me being lazy, that's just canon.
• -o outputfile — override the output filename that's sitting in the configuration file.

🫶 pro tip bestie: dawg will read stdin if the filename is "-".

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🌸 FILE FORMAT 🌸

so the file format is a whole series of statements shaped like "name = value," where "name" is alphanumeric and value can be a string, a number, a boolean, a tree, or a vector of values. and here's the cute part: a single variable is equivalent to a vector of a single entry. one-item vector, same energy. 🎀

• string: "[char-sequence]"

or '[char-sequence]'

or """[multi-line char-sequence]""" (rm initial and final newlines)

or '''[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, ...}

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👑 OPTIONS 👑

every single one of these config keys, with her type and her job description. no skips, no summaries, we're doing the whole list. 🌈

• 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.*

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📜 LICENSE 📜

okay legal bestie moment, but it's genuinely good news: 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. slay. 💜

it's distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY — not even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. that's not a vibe check, that's just how it is. 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:

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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and that's the whole page, bestie 💖 — this was dawg 1.2-release, dated December 2015, closing out the DAWG(1) era with main character energy. go simulate some DNA. 🦋✨