• Visualizing a dated Open Tree

    There have been plenty of posts here about the Open Tree of Life. As part of a broader attempt to date the Open Tree of Life (discussed here), I have made a figure. Feel free to use it as you like! I will update with additional information periodically.

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  • Dating OpenTree

    The Open Tree of Life is a great resource that brings together taxonomy, phylogenies, and a nice API that can be used for several purposes. One current limitation of the resource are branch lengths. For seed plants, Joseph W. Brown and I recently published a paper (discussed here) that combines Open Tree taxa with GenBank data and estimates divergence times. However, this was just for seed plants.

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  • Big Botany Tree

    Recently Joseph Brown and I constructed a large tree for seed plants (see publication here). To do this, we used a program called PyPHLAWD and several scripts to add the Open Tree of Life taxa that aren’t represented in GenBank back into the phylogeny.

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  • Reverse complements

    Reverse complements can be the bane of any informatics projects. High-throughput sequence processing and alignment projects need to be confident that reverse strand sequences are corrected or else the results of the analyses will be junk. There are a number of ways that researchers attempt to overcome these problems. Here, I won’t discuss all of these ways but instead will discuss some of the solutions that have been coded into phyx and contrast them with the nice options in mafft .

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  • phyx update 0

    I plan on being a little more verbose about the updates to the software in my GitHub and bitbucket repos. They will probably be brief unless I start to ramble.

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  • Open Tree toys

    The Open Tree of Life has produced several fantastic resources for the phylogenetics community including a comprehensive taxonomy that is immediately useful for phylogenetic purposes (i.e., doesn’t have incertae sedis), a comprehensive and perpetually-updating phylogeny that includes all named species (present in the aforementioned taxonomy), a tree store that contains thousands of phylogenetic trees that have been mapped to the common taxonomy and therefore can be used for any number of comparative purposes, and a number of computational tools to interact with all these resources or construct your own comprehensive tree of life.

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