DNASTAR

What multiple sequence alignment methods are available for DNA and protein?

MegAlign Pro’s multiple sequence alignment tools for DNA and protein include Clustal Omega, Clustal W, MAFFT, and MUSCLE.

Is a multiple genome alignment method available?

Yes. MegAlign Pro’s Mauve algorithm has high capacity and uses MUSCLE to perform block alignments of microbial genomes. This algorithm was developed in the Genome Evolution Laboratory at the University of Wisconsin-Madison.

What is a profile alignment?

Profile alignments merge two existing multiple alignments without removing any of the existing gaps. However, new gaps may be automatically inserted to reconcile the new alignment.

What methods does MegAlign Pro offer for computing phylogeny?

MegAlign Pro offers two methods for generating phylogenetic trees: RAxML, for computer Maximum Likelihood trees, and the Neighbor Joining method, which uses the BIONJ algorithm.

Can I apply bootstrapping to phylogenetic trees?

Yes, MegAlign Pro supports bootstrap analysis using the RAxML method for Maximum Likelihood trees. To perform bootstrapping, first perform an alignment and then create a Maximum Likelihood tree. In the RAxML options dialog, check the Bootstrap analysis checkbox. You can adjust the number of iterations and the seed to refine and reproduce bootstrap values.

Does MegAlign Pro support multiple phylogenetic trees in a single project?

Yes. MegAlign Pro makes it easy to to have multiple trees for a single alignment, so that you can easily compare using different phylogenetic methods or changes to the alignment.

Can I export my phylogenetic tree?

Yes. You can export your tree in either Newick or Nexus formats that are compatible with third part tree editing programs like FigTree by selecting File > Export Data > Tree.

You can also export an image of your phylogenetic tree in Adobe PDF (.pdf), Microsoft PowerPoint-optimized (.pptx), PNG image (.png) or JPG (.jpg, .jpeg) formats by selecting File > Export Image > Tree or clicking on the camera icon from the Tree view.

How do I export an image of my multiple sequence alignment?

Choose File > Export Image > (View Name) and choose the export format: Adobe PDF (.pdf), Microsoft PowerPoint-optimized (.pptx), PNG image (.png) or JPG image (.jpg, .jpeg).

Can I modify my multiple sequence alignment?

Lasergene’s multiple sequence alignment software, MegAlign Pro, supports multiple ways to modify an alignment. You can:

• Trim ends at the beginning or end of an alignment.
• Realign a range of aligned sequences using different parameters or a different alignment engine.
• Merge two existing completed alignments together.
• Add all/selected sequences from the “Unaligned Sequences” area into the current alignment, while retaining all of the gaps of the original, pre-merge alignment.
• Realign existing aligned sequences plus selected unaligned sequences

Can I modify individual sequences within my multiple sequence alignment?

Yes. MegAlign Pro gives you the ability to reverse complement, edit, and trim individual sequences within an alignment.

What’s the easiest way to find sequence matches for my consensus sequence?

MegAlign Pro’s Search wizard, accessed using Search > Sequence Search, lets you search a query sequence against one of NCBI’s BLAST databases. The sequence can be part or all of an active sequence, another sequence file on your computer, or typed/pasted-in text.

Can I map features from an annotated source sequence to a closely related sequence?

MegAlign Pro’s feature mapping (Features > Map Features) commands let you map a single annotation or all annotations from a source sequence to a target sequence. The sequences involved must have been previously aligned. During the process, you may optionally filter annotations so as to include/exclude specific gene types. Feature mapping is most commonly used to map desired annotations from a “completely annotated” sequence to a closely-related but “incompletely annotated” one.

Can I perform a MUSCLE alignment with multi-segment sequences?

Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment sequences. When you enter a group of sequences into MegAlign Pro using the File > Add Sequences End-to-end command instead of the standard File > Add Sequences command, the entire data set will be concatenated end-to-end and treated as a single multi-segment sequence.

What’s the best way to add gapped sequences to my multiple sequence alignment project?

To import gapped sequences from an existing MegAlign Pro file, use File > Open and choose the .msa file. Once the project is open, select all the sequences, then use Align > Unalign Selected.

To import gapped nucleotide sequences from another type of file, use SeqMan Pro to remove the gaps. Launch SeqMan Pro, then drag and drop the gapped sequence file(s) onto the SeqMan Pro window. Select all sequences, then choose Contig > Export Sequences > Single File. Select either FastA or GenBank Flat File format and choose a file name and location. Make sure that Include gaps is left unchecked, and then click Save. The sequence(s) in the newly saved file can now be added to MegAlign Pro in the usual way.

Which alignment method should I use for my multiple sequence alignment?

For gene-level alignment of either protein or nucleotide sequences, use  Clustal Omega, Clustal W, or MAFFT. They offer editable options for speed, capacity, algorithm, etc., and are the only methods available for “profile” alignments. The disadvantages to gene-level aligners is that sequences must be on same strand, and that large rearrangements (e.g., inversions, translocations) are not allowed. For genome-level alignment of nucleotide sequences, use Mauve. Mauve has high capacity and uses MUSCLE to create multiple alignments for each block that contains more than a single sequence.