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

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.

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.

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.

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.