Data and supplementary information from: Sequential bayesian phylogenetic inference

The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost. Instead, phylogenetic pipelines generally consist of sequential analyses, whereby a single point estimate from a given analysis is used as input for the next analysis (e.g., a single multiple sequence alignment is used to estimate a gene tree). In this framework, uncertainty is not propagated from step to step, which can lead to inaccurate or spuriously certain results. Here, we formally develop and test the sequential approach for Bayesian phylogenetic inference, which uses importance sampling to generate observations for the next step of an analysis pipeline from the posterior produced in the previous step. The sequential approach presented here not only accounts for uncertainty between analysis steps, but also allows for greater flexibility in software choice (and hen..., , , # Sequential Bayesian Phylogenetic Inference

## Empirical Data Analysis (Divergence Times of Insects)

The data are retrieved from Misof, Bernhard et al. (2015). Data from: Phylogenomics resolves the timing and pattern of insect evolution [Dataset]. Dryad. [https://doi.org/10.5061/dryad.3c0f1](https://doi.org/10.5061/dryad.3c0f1)

This repository contains five files from that study, where we simply transformed the data into a different file format. The files are:

1. BLOSUM62.nex, JTT.nex and LG.nex which contain the amino acid dataset for the empirical amino acid substitution model analysis.
2. supermatrix_C.nuc.all.fas which contains the DNA supermatrix
3. supermatrix_D.phy which contains the amino acid supermatrix in Phylip format for PhyloBayes.