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CASTLES

CASTLES is a method for estimating branch lengths of a given species tree from estimated gene trees in the unit of expected number of substitutions per sequence site (substitution units), that addresses gene tree heterogeneity due to incomplete lineage sorting (ILS), as modeled by the multi-species coalescent (MSC) model.

The CASTLES algorithm is described in the following paper:

Y. Tabatabaee, C. Zhang, T. Warnow, S. Mirarab, Phylogenomic branch length estimation using quartets, Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i185–i193, https://doi.org/10.1093/bioinformatics/btad221

Datasets and results from this study are available in CASTLES-paper repository.

Update: This is an old README for CASTLES. The new README is here.

Dependencies

CASTLES is implemented in Python 3. It was developed and tested in Python version 3.7.0 and has the following dependencies:

Usage Instructions

Input: A file containing a species tree and a file containing a set of single-copy or multi-copy gene trees, both in newick format.

Output: A file containing the species tree in newick format, annotated with substitution unit (SU) branch lengths.

Running CASTLES is currently a two-step approach, but in the future it will be integerated inside the species tree estimation software ASTER and can be used with both ASTRAL and ASTRAL-Pro.

  1. Annotate branches of the species tree with quartet statistics using ASTER.
  2. Assign final branch lengths to each branch of the species tree using castles.py.

Annotating the input species tree with ASTER

Follow the installation instructions on ASTER repository and download ASTER (>= v1.13.2.4).

For single-copy gene trees, use the following command to compile ASTER

$ g++ -std=gnu++11 -D"ASTRALIV" -march=native -Ofast -pthread src/astral.cpp -o bin/astral_castles

For multi-copy gene trees, use the following command for compilation

$ g++ -std=gnu++11 -march=native -D CASTLES -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro_castles

WARNING: If you use an M1 Mac and you got a compilation error with the command above, we suggest you switch to a Linux system.

Then, use the following command to run ASTER, where the annotated tree is printed to the log file

$ astral_castles -C -i <gene_tree_path> -c <species_tree_path> -o <output_path> > annotated.tre

or the following command for multi-copy gene trees

$ astral-pro_castles -C -i <gene_tree_path> -c <species_tree_path> -o <output_path> > annotated.tre

If an outgroup taxon is known, it can be specified with the option --root as follows

$ astral_castles -C -i <gene_tree_path> -c <species_tree_path> -o <output_path> --root <outgroup_taxon> > annotated.tre

Handling multiple individuals per species

When there are multiple individuals per species and the individual names do not match the species names, run the following command

$ astral_castles -C -i <gene_tree> -a <name_map> -c <species_tree> -o <output_path> > annotated.tre

where the name_map file contains maps from individual names to species names in the following format

individual_name1    species_name1
individual_name2    species_name2
individual_name3    species_name3
...

Assigning SU branch lengths

Use the following command to produce the final species tree with SU branch lengths (note: the input is the ASTER-annotated tree, not the original species tree)

$ python3 castles.py -t annotated.tre -g <gene_tree_path> -o <output_path>

Arguments

  • Required
 -t,  --speciestree        ASTER-annotated species tree in newick format
 -g,  --genetrees          input single-copy gene trees in newick format
 -o,  --output             output file containing a species tree annotated with SU branch lengths

Example

The example directory contains a 30-taxon model species tree and a corresponding tree annotated by ASTER, and 500 estimated gene trees. The command below shows how CASTLES can be run on this data:

$ python3 castles.py -t example/aster.trees.annotated -g example/estimatedgenetre.gtr -o example/castles.tre