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MegAlign Pro
MegAlign Pro offers a complete sequence alignment software package, including everything you need for each stage of an alignment – not only the algorithms needed for aligning both gene-level and genome-scale sequence data, but also the capability to dig deep in the post-alignment stage.

Comprehensive
“Most comprehensive and full-feature alignment software I have found.”

including the ability to batch clone groups of fragments simultaneously, and guides you step-by-step in preparing your vectors and amplifying your inserts using all of the most popular cloning methods: Gateway, Gateway Multisite, Gibson, GeneArt, In-Fusion, TA, TOPO, and PCR-

Supported workflows include performing multiple and pairwise sequence alignments, phylogenetic analysis, assembling contigs of Sanger sequences, creating virtual clones, designing primers, and more.
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