pcms

Phylogenetic Covariance Matrix Sparisifcation

Installation

To install the pcms package, clone this GitHub repository and, inside the repository, run

./build.sh && ./build.sh --clean

This package requires the mvhg package, which can be installed with

mkdir -p lib/ && cd lib/
git clone git@github.com:spsvihla/mvhg.git && cd mvhg/
./build.sh && ./build.sh -- clean

Datasets

Greengenes reference database and phylogeny

We make use of the Greengenes database [1-2], the most up-to-date version of which can be found under /greengenes_release/current at the link provided. As an example, the gg_13_8 dataset can be downloaded as follows:

wget https://ftp.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz
tar -xzf gg_13_8_otus.tar.gz

Guerrero Negro microbial mat samples

Other notebooks use the Guerrero Negro microbial mat datasat collected and analyzed by Harris, Caporaso, et al. [3]. In particular, the sequences available on GenBank are used to pick OTUs clustered against the Greengenes database as described in [3]. These data can be downloaded at the link provided by selecting Send to > Gene features above the search results and creating a file with the "FASTA Nucleotide" format.

Note: The above analysis is for the full-length Sanger sequences. The corresponding table for the 454 partial-length sequences described in the paper may be found on Qiita.

Data directory structure

The notebooks in this respository are written assuming the following directory structure:

$DATA/
├── greengenes/
│   ├── gg_13_5_otus/
│   │   └── <contents of gg_13_5.tar.gz>
│   ├── gg_13_8_otus/
│   │   └── <contents of gg_13_8.tar.gz>
│   └── ...
└── greengenes2/
    ├── gg_22_10_otus/
    |   ├── 2022.10.phylogeny.id.nwk
    │   └── ...
    └── ...

Other Information

We have provided a Mathematica notebook used in the original publication of this work.

References

1. McDonald, D. et al. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol 42, 715–718 (2024). https://doi.org/10.1038/s41587-023-01845-1
2. McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139
3. Kirk Harris, J. et al. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. The ISME Journal 7, 50–60 (2013). https://doi.org/10.1038/ismej.2012.79.
4. Svihla, S. and Lladser, M. E. Sparsification of Phylogenetic Covariance Matrices of Critical Beta-splitting Random Trees. In preparation.
5. Gorman, E. & Lladser, M. E. Sparsification of large ultrametric matrices: insights into the microbial Tree of Life. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479, 20220847 (2023). https://doi.org/10.1098/rspa.2022.0847