Sequences that consist of more than one chromosome, contig, or fragment are called multi-segment files.

Suppose you want to string together the consensus sequences from all the contigs in an assembly, or chromosomes in a genome, or exons in a gene, etc. If you enter these sequences using File > Enter Sequences or the corresponding button ( ), you will end up aligning the parts to one another. By entering these sequences into MegAlign Pro using the procedure in this tutorial, the entire set of sequences in the multi-segment file (or set of files) will instead be treated as an end-to-end concatenation.

Begin with Part A: Add and align multi-segment files.

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