pegi3s/aster repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of ASTER⁠, a family of optimization algorithms for species tree inference from gene trees, genome alignments, raw reads, and other phylogenomic data.

ASTER includes:

• ASTRAL-IV
• ASTRAL-Pro3
• Weighted ASTRAL
• CASTER-site
• CASTER-pair
• WASTER
• D* statistic

⁠Using the ASTER image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster <tool_binary> -i /data/input_file -o /data/output_file

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• <tool_binary> with the ASTER tool you want to execute (e.g., astral4, astral-pro3, wastral, caster-site).
• input_file - to the actual name of your input file.
• output_file - to the actual name of your output file.

ASTRAL-IV

ASTRAL-IV infers an unrooted species tree from a set of gene trees under the Multi-Species Coalescent model, and is designed to scale to large phylogenomic datasets while handling incomplete lineage sorting and missing taxa.

If you want to run astral4, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster astral4 -i /data/genetree.nw -o /data/species_tree_astral4.tre

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• genetree.nw - to the actual name of your input file (.nw).
• species_tree_astral4.tre - to the actual name of your output file (.tre).

ASTRAL-Pro3

ASTRAL-Pro3 infers an unrooted species tree from multi-copy gene trees (including paralogs and orthologs) under the Multi-Species Coalescent model, providing a faster and more memory-efficient implementation with branch length estimation in substitution-per-site units.

If you want to run astral-pro3, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster astral-pro3 -i /data/multitree.nw -o /data/species_tree_astral-pro3.tre

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• multitree.nw - to the actual name of your input file (.nw).
• species_tree_astral-pro3.tre - to the actual name of your output file (.tre).

Weighted ASTRAL

Weighted ASTRAL infers species trees from gene trees using threshold-free weighting schemes (based on branch support and/or branch length) to reduce the impact of low-confidence signals and improve accuracy over the standard unweighted ASTRAL approach.

If you want to run wastral, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster wastral -i /data/genetree.nw -o /data/species_tree_wastral.tre

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• genetree.nw - to the actual name of your input file (.nw).
• species_tree_wastral.tre - to the actual name of your output file (.tre).

CASTER-SITE

CASTER-site infers species trees directly from genome-wide alignments using site pattern information, providing a scalable, gene-tree–free method that is statistically consistent under the MSC model and highly efficient for large phylogenomic datasets.

If you want to run caster-site, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster caster-site -i /data/genetrees.tre_1.fas -o /data/species_tree_caster-site.tre

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• genetrees.tre_1.fas - to the actual name of your input file (.fas, .phy).
• species_tree_caster-site.tre - to the actual name of your output file (.tre).

CASTER-PAIR

CASTER-pair infers species trees from genome-wide alignments using pairwise site patterns, offering a scalable and statistically consistent alternative to gene tree–based methods for large-scale phylogenomics.

If you want to run caster-pair, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster caster-pair -i /data/example.phylip -o /data/species_tree_caster-pair.tre

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• example.phylip - to the actual name of your input file (.fas, .phy).
• species_tree_caster-pair.tre - to the actual name of your output file (.tre).

WASTER

WASTER is a coalescent-aware species tree inference tool that works directly from raw sequencing reads (e.g., FASTQ), calling SNPs and then using CASTER to reconstruct accurate species trees — even from low-coverage data.

If you want to run waster, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster waster -i /data/input_list.txt -o /data/species_tree_waster.tre

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• input_list.txt - to the actual name of your file containing a list of input files (.fa, .fq).
• species_tree_waster.tre - to the actual name of your output file (.tre).

D*statistic

D*statistic detects signals of introgression (gene flow) between species by computing sliding-window statistics from genome alignments.

If you want to run dstar, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/aster dstar /data/ape.fa /data/mapping.tsv 10000 > slidingwindow.tsv

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• ape.fa - to the actual name of your input file (.fa, .fas or .fasta).
• mapping.tsv - to the actual name of your mapping file (.tsv).
• slidingwindow.tsv - to the actual name of your output file (.tsv).

⁠Using a Mapping File

Some tools (e.g., ASTRAL-IV, ASTRAL-Pro3) use a gene-to-species mapping file.

In that case, include the -a option:

docker run --rm -v /your/data/dir:/data pegi3s/aster <tool_binary> -i /data/input_file -a /data/mapping_file.map -o /data/output_file

In this command, you should replace:

• /your/data/dir to point to the directory that contains your input data.
• <tool_binary> with the ASTER tool you want to execute (e.g., astral4, astral-pro3, wastral).
• input_file - to the actual name of your input file.
• mapping_file.map -to the actual name of your mapping file (.map).
• output_file - to the actual name of your output file.

To see the ASTER⁠ help, just run: docker run --rm pegi3s/aster <tool_binary> --help