Data and code from: Efficient inference of macrophylogenies: Insights from the avian tree of life

The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling > 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the “fast” maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) su..., , , # Data and code from: Efficient inference of macrophylogenies: Insights from the avian tree of life

[https://doi.org/10.5061/dryad.5dv41nsgw](https://doi.org/10.5061/dryad.5dv41nsgw)

## Description of the data and file structure

This dataset contains the data and code to estimate macrophylogenies using various approaches (supermatrix, filtered supermatrices, supertree, divide-and-conquer, and coalescent species tree method), compare their phylogenetic accuracy and computational requirements and perform divergence time estimation.

### Files and variables

#### File: alignments_final_trimmed_clean.zip

**Description:** This file contains individual alignments for the full dataset.

#### File: filtered_concatenated_files.zip

**Description:** This file contains 27 concatenated sequence data files for the filtered datasets. 

#### File: treefiles.zip

**Description:** This file contains several subfolders.

1\. initial exploration, which includes tree files produced by different approac...,