Constructing a MegaPhylogENy for phylogenetic analysis

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For my research project I wanted to construct a phylogeny containing diverse plant taxa using pre-existing DNA sequences. The basic pipeline sounded easy enough. I would download the sequences I wanted from GenBank, align them, and then put the alignment into a phylogenetic software program, such as BEAST.  Easy, right? Well 6 months later I can tell you that it is easy but upon doing it for the first time I faced many hiccups along the way that I want to share through a series of blog posts.

The following series of blog posts (although published out of order) will address each of these hiccups:

1.     Existing available software for constructing a megaphylogeny

2.     Downloading DNA sequences from the NCBI’s genbank database—Let’s automatic this task!

3.     GenBank isn’t as straight-forward as you may think—Querying for genes of interest