DNADynamo can generate and display Global Multiple Sequence Alignments via Clustalw or Muscle, and also provides a
sophisticated alignment editor for correcting alignments and/or generating 'hand made' alignments
Clustal W (and MUSCLE) are free 'academically developed' software that performs multiple sequence alignments on DNA and
Protein Sequences. You may also be familiar with ClustalX - A Graphical User Interface to the ClustalW software.
DNADynamo can send your sequences to ClustalW or MUSCLE for alignment and display the ClustalW / MUSCLE output files,
conveniently integrating DNADynamo with ClustalW / MUSCLE.
In DNADynamo's 'paged' display output, annotations are displayed and can be added to the sequence alignments, integrating
BLASTs, genbank annotations, user defined annotations and annotated clustalw /muscle multiple alignments. Coloured and
annotated alignments can be printed to pdf for publication or further import and modification in dedicated illustration software.
DNADynamo also provides a 'linear' alignment editor which supports mouse drag editing, making it easy to manually correct
alignments generated by clustalw/muscle, or generate a complete 'hand made' alignment. When this editor is loaded with a DNA
alignment, you can display a correspondingly translated protein alignment, similar to the functionality provided by SE-AL software.
Using these functions it is possible to align the DNA sequences with respect to their protein translation, rather than just to the DNA
sequence itself, which some researchers believe generates a more meaningful alignment for input into phylogenetic tree software.
With respect to this, DNADynamo will also takes a bunch of DNA sequences, translate them, generate a protein alignment, and
then re-assemble a DNA alignment based on the protein alignment, which takes much of the work out of generating such
translation respecting DNA alignments. The alignments can be output as FASTA files or NEXUS files for input into phylogenetic
example alignment in
DNADynamos 'paged' display
which includes annotated
sequences. A linear alignment
editor that supports mouse drag
editing and simultaneous dna-
>protein alignments is also