Phylogenetics in the microbiome with SuchLinkedTrees

In the last article, we saw how to use SuchTree to probe the topology of very large trees. In this article, we're going to look at the other component of the package, SuchLinkedTrees.

If you are interested in studying how two groups of organisms interact (or, rather, have interacted over evolutionary time), you will find yourself with two trees of distinct groups of taxa that are linked by a matrix of interaction observations. This is sometimes called a 'dueling trees' problem.

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SuchTree, much article

There are a lot of packages for working with and manipulating phylogenetic trees using python. Rather than compete with packages like dendropy and ete3 on the basis of features, SuchTree does one thing well -- its memory usage and algorithmic complexity linearly with the number of taxa in your tree. If you need to work with very large trees, this is very helpful.

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