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minor suggested edits to multiple-sequence-alignment.md in fundamentals #294

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AstrobioMike
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mostly a few suggestions i think help the reader follow along more easily;
also added key='id' to the distance matrix call when comparing the inital tree to the msa tree to keep the labels

Great chapter!

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@AstrobioMike, thanks for the PR. Just a couple of small requests for changes on this one and it'll be ready for merge.

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incorporating some more edits/wording changes, including issue [applied-bioinformatics#296](applied-bioinformatics#296)
@gregcaporaso gregcaporaso force-pushed the master branch 2 times, most recently from 04fd354 to 8613ff2 Compare October 2, 2018 02:29
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