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Welcome to MegAlign Pro
Welcome to MegAlign Pro
MegAlign Pro is Lasergene’s application for generating multiple and pairwise alignments of protein and/or nucleic acid sequences using your choice of alignment methods. Easily navigate between synchronized views with a click of a button, and rearrange views and…
Try it! – Add and align multi-segment sequences
Sequences » Add multi-segment sequences to a project » Try it! – Add and align multi-segment sequences
The following video tutorial describes how to add multi-segment sequences and then align them using the MUSCLE multiple alignment algorithm. If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file…
When no document, or a blank document, is open
MegAlign Pro Interface » Panels » Details panel » When no document, or a blank document, is open
When no document or only a blank document (one containing no sequences) is open, the Details panel displays links to help you get started in MegAlign Pro. Heading One or more links are available. The first three options are available for blank…
Places panel
MegAlign Pro Interface » Panels » Places panel
The Places panel lets you quickly navigate to a sequence location or range that you have visited before. The following video shows how to bookmark favorite locations using the Places panel: To open the Places panel: Click on the Places tab (). If the panel is not…
Modify a multiple alignment
Perform a Multiple Sequence Alignment » Modify a multiple alignment
The following table describes ways to modify an initial multiple alignment: Task See this topic To realign a range of aligned sequences using different parameters or a different alignment engine Subalign sequences To merge two…
Perform a Multiple Sequence Alignment
Perform a Multiple Sequence Alignment
MegAlign Pro supports the following multiple sequence alignment methods: Clustal Omega, Clustal W, MAFFT, MUSCLE and Mauve. Click here for descriptions and a comparison of the different methods. To learn how to perform, modify, and troubleshoot multiple sequence…
Import an alignment from another application
Create or Open a Project » Import an alignment from another application
To import an alignment from another applicaton: Do either of the following: From the Welcome tab, click Open Project on the left. Then use the option Import alignment on the right. Choose File > Import Alignment. Navigate to the file you wish to…
Open an existing project
Create or Open a Project » Open an existing project
To open an existing MegAlign Pro project (.msa): Do any of the following: From the Welcome tab, click Open Project on the left. Then use the options on the right to Open alignment project or open a recent document. Drag an .msa file from the file explorer…
Sequences
Sequences
You can add the following types of sequences to a MegAlign Pro project: Ungapped sequences, including SeqNinja files Gapped sequences Automatic translations of nucleotide sequences Only sequences that meet filtering thresholds Multi-segment…
Mauve alignment options
Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Multiple sequence alignment methods and options » Mauve alignment options
The Mauve alignment algorithm is for genome level alignment of nucleotide sequences. To run a Mauve alignment, select two or more nucleotide sequences and choose Align > (Re)Align Using Mauve. If you wish to change method options, instead choose Align > Align with…
Export an image of the view
Export » Export an image of the view
To export an image of a view : Choose File > Export Image > (View Name) or click the Export image tool ( ) at the upper right of a view that allows exporting. Specify the file name and choose the export format: Adobe PDF (.pdf), Microsoft…
Map features (copy features to another sequence)
Features » Map features (copy features to another sequence)
MegAlign Pro’s feature mapping lets 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…
Tracks
Tracks
“Tracks” are rows of information that can be displayed or hidden, as desired, in the Overview and Sequences view. Tracks can pertain to a header, footer, or individual sequence row. The following video provides a brief overview of how tracks are used in…