Create a script to use as MegAlign Pro input

MegAlign Pro is Lasergene’s application for performing multiple alignments of large DNA, RNA, or protein sequences using one of three alignment methods: MUSCLE, Mauve, or Clustal Omega. MegAlign Pro also offers several post-alignment analysis tools, including phylogenetic tree generation and access to a distance matrix, showing distances between each pair of sequences.

When you use MegAlign Pro, you need to enter the sequences you wish to align. It is possible to add a SeqNinja .star project file in lieu of the usual sequence files. The advantage of adding a .star project to MegAlign Pro is that it will always call up the most up-to-date version of the input data for use in making its output. So, if you change, add, or delete the input data that the .star file points to, the .star file will update this information in MegAlign Pro.

When you use a SeqNinja Project (.star) file as input for MegAlign Pro, note that the project is read as a “set of sequences,” and is not actually executed, meaning no sequence files are written. This type of project has limitation that any input files referenced in the script must already exist. In other words, the script should not reference an input file that doesn’t exist until it is created earlier in the same script. Instead:

• Replace all the references to the input file with a variable (e.g., $a), or…

• Create a SeqNinja script to create the necessary files and run the script. Then, in the SeqNinja script you wish to add to MegAlign Pro, reference those already-created files.

When creating a SeqNinja script for use as MegAlign Pro input, you may break statements into multiple lines before or after the following operators:

For examples, any of the following SeqNinja steps (as they appear in the Text view) would be read as a set of sequences in MegAlign Pro:

Example 1:

$a = $b
+ $c

Example 2:

$a = $b +
$c

Example 3:

$a = sample("myfile.fasta",
from=100,
to=200)