Phylogenomics

Phylogenomics sits within phylogenetics and addresses tree-of-life inference from genome-scale data. The page below sketches the conceptual scope of the area, the methodological tools it relies on, and the recent literature anchoring its current frontier.

The area organises around a small number of recurring axes: scope (what biological scales the work spans), method (the dominant experimental or computational tools), data regime (what kinds of measurements are now routine vs. still frontier), and open questions (what the field cannot yet do reliably). The sources below cover different combinations of these axes.

Foundational references

Felsenstein, Inferring Phylogenies is a standard reference for the foundations covered here, used across the field to anchor terminology, canonical models, and the relationships between sub-areas of phylogenomics. Treat it as the entry point to which the more specialised work below adds frontier detail.

Frontier results

A primary recent reference for this area is RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies (Stamatakis, 2014), which contributes to the methodological or empirical conversation that defines the current frontier of phylogenomics. It illustrates the kind of question the field is actively pursuing — the specific technical claim, the dataset or system on which it was validated, and the way subsequent work builds on it.

Open questions

Open questions in phylogenomics cluster around scaling current methods to larger systems, integrating measurements across modalities, and producing predictive rather than descriptive models. The references above mark the work that the next iteration of this page should engage with in more specific detail.