DNADynamos ClustalW Interface

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 software.

example alignment in DNADynamo's 'paged' display which includes annotated sequences. A linear alignment editor that supports mouse drag editing and simultaneous dna->protein alignments is also provided