dna_sequence_aligner assumes you have a template dna sequence. All other DNA sequences are matched up with the template and then they are all merged into one template-centric alignment. The output was custom designed to show coverage at a glance in a template-centric fashion.
The software is also written so that you can annotate your template fasta file with comments (must lead with a '#' character).
Clustalw must be installed (clustalw package in ubuntu/debian) and generally accessible.
[Bioruby is heavily relied on, but it is explicitly stated as a gem dependency so you shouldn't have to worry about it if installed by gem]
The executable is the main item of interest. It takes one (or more) sequence files. Your template should be the first fasta encountered.
dna_sequence_aligner template.fasta others.fasta > output.aligned.txt # sequences in separate files dna_sequence_aligner template.fasta other1.fasta other2.fasta > output.aligned.txt # all sequences in one file (template first) dna_sequence_aligner all_seqs.fasta > output.aligned.txt
A comment (#) aware DNA sequence translator is provided to check and see if things are in register and so forth. It outputs the DNA sequence and protein sequence below it.
# -s 2 is a 2 nucleotide frameshift dna_translator.rb -s 2 dna_annotated.fasta > protein.txt
all gaps <blank> template gap ^ gap below template . agreement = all bad matches ^ non-consensus ?
This is very much alpha software at the moment. It was written in a time crunch and so it is a little rough around the edges. However, key components have specs written and appear to work properly. If I have to do more alignments or you send me pull requests then this may get to be nicer software.