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Console panel

MegAlign Pro Interface » Panels » Console panel

The Console panel displays information, messages and warnings about the operation in progress, or an operation that was recently performed. To display the console for a particular project: Click the tab with the project name, then open its console using the View >…

Troubleshooting “wrong type” or “too long” errors

Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Troubleshooting “wrong type” or “too long” errors

Error message that sequences are the wrong type or are too long: After beginning an alignment, an error message will appear if the sequences are not of the appropriate type or are too long for the selected algorithm. If performing a MUSCLE or Clustal Omega alignment,…

Perform an initial multiple sequence alignment

Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment

To perform the initial multiple sequence alignment: Select three or more sequences to align, or select nothing if you want to align all sequences. (Note: If you choose just two sequences, or if only two are present, you will be prompted to instead do a pairwise…

Pairwise alignment for sequences with similar lengths

Perform a Pairwise Sequence Alignment » Pairwise alignment for sequences with similar lengths

The following instructions describe how to align sequences with similar lengths (i.e., within one or two orders of magnitude). DNASTAR has used these pairwise algorithms in this workflow to successfully align protein sequences up to 35,000 bases in length. *Note: If…

Troubleshooting “fatal error” in Clustal Omega alignments

Perform a Multiple Sequence Alignment » Perform an initial multiple sequence alignment » Troubleshooting “fatal error” in Clustal Omega alignments

Clustal Omega requires that each sequence in an alignment contain at least one residue that is not an ambiguity code. DNA sequences must contain at least one A, C, T or G. RNA sequences must contain at least one A, C, U, or G. Protein sequences must contain at…

Perform a Gene Homology Alignment

Perform a Gene Homology Alignment

The ability to do gene homology alignments was added in Lasergene 17.6, released in early 2024. This method is for nucleotide sequences only and is set up using a simple wizard with five screens. With this method, you can perform a phylogenetic analysis of much larger…

MegAlign Pro Interface

MegAlign Pro Interface

MegAlign Pro displays your sequences and results in customizable views and panels. The items displayed in the window, their locations, colors, fonts, etc. can all be changed to suit your preferences. To learn more, see the following topics: Welcome screen…

Part A: Add and align multi-segment files

Perform a Multiple Sequence Alignment » Try it! – Perform a MUSCLE alignment with multi-segment sequences » Part A: Add and align multi-segment files

If you have not yet downloaded and extracted the tutorial data, click here to download it. Then decompress (unzip) the file archive using the method of your choice. If a MegAlign Pro project is already open, choose File > New Alignment Project > Blank Document.…

Panels

MegAlign Pro Interface » Panels

Settings panels allow you to optimize the look, contents and layout of the MegAlign Pro window. To learn what can be done within each panel and the expandable “sections” within each panel, click the links…

Output files

Features » Map features (copy features to another sequence) » Output files

After running the Map Features step, the output consists of several files. File Name Notes PROJECT_map_features_console.txt Copy of the text that appeared for this mapping in the Console side panel in the MegAlign Pro user interface.…