PhyloSort vs. Traditional Methods: Speed, Accuracy, and Scalability

PhyloSort Tutorial: From Installation to Advanced Tree FilteringPhyloSort is a command-line tool designed to help researchers sort, filter, and manipulate phylogenetic trees at scale. This tutorial walks through installation, basic usage, common workflows, and advanced tree-filtering techniques. Examples use Newick-formatted trees and common bioinformatics file types. Commands and scripts are shown for Unix-like systems (Linux, macOS). Adjust paths and tool names for your environment.

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Table of contents

1. Overview and use cases
2. Installation
3. Input and output formats
4. Basic commands and options
5. Common workflows
6. Advanced tree filtering techniques
7. Performance and scalability tips
8. Troubleshooting and best practices
9. Example pipelines
10. References and further reading

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1. Overview and use cases

PhyloSort is built to automate repetitive operations on phylogenetic trees and to scale filtering and sorting across large datasets. Typical use cases:

• Extracting subtrees that contain specific taxa or clades
• Filtering out trees based on topology criteria (e.g., monophyly, presence/absence of taxa)
• Ranking trees by support values or other metrics
• Batch-processing hundreds to thousands of gene trees for phylogenomic analyses

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2. Installation

Prerequisites:

• Python 3.8+ (common), or the language runtime the PhyloSort build targets
• Standard Unix command-line tools (bash, awk, sed) for example pipelines
• Optional: conda or virtualenv for isolated installations

Installation methods (choose one):

• Pip (recommended if available):

  pip install phylosort 

• Conda (if available on conda-forge):

  conda install -c conda-forge phylosort 

• From source (if repository available):

  git clone https://example.org/phylosort.git cd phylosort python setup.py install 

After installation, verify with:

phylosort --version 

Expected output: a version string confirming installation.

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3. Input and output formats

Common input formats:

• Newick (.nwk, .newick) — standard for many tree-building tools
• Nexus (.nex) — occasionally supported
• Tabular lists of taxa to match or exclude (plain text)

Common outputs:

• Filtered Newick trees
• Summary reports (CSV or TSV) with per-tree metrics (e.g., number of taxa, support statistics)
• Extracted subtree files

Example input tree (Newick):

((Homo_sapiens:0.2,Pan_troglodytes:0.21)0.95,Mus_musculus:0.5); 

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4. Basic commands and options

Typical phylosort command structure:

phylosort [command] [options] <input> -o <output> 

Common commands:

• filter — keep or remove trees matching criteria
• extract — pull out subtrees containing specified taxa
• stats — produce summary statistics across a set of trees
• sort — rank or order trees by a metric

Example: filter trees that contain both Homo_sapiens and Pan_troglodytes:

phylosort filter --require "Homo_sapiens,Pan_troglodytes" trees_dir/*.nwk -o filtered/ 

Expected output: filtered/newick files containing only trees that match.

Example: extract the subtree for primates and write to a new file:

phylosort extract --taxa "Homo_sapiens,Pan_troglodytes" input.nwk -o primates_subtree.nwk 

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5. Common workflows

• Single-gene tree filtering: remove trees lacking a minimum taxon set or minimum bootstrap support.
• Phylogenomic matrix construction: only retain gene trees where target species are present to fill a species-by-gene presence matrix.
• Detecting horizontal gene transfer: filter trees where expected species are non-monophyletic or deeply nested in unexpected clades.

Example: filter trees with at least 10 taxa and average bootstrap >=70:

phylosort stats trees/*.nwk --min-taxa 10 --min-avg-bootstrap 70 -o pass_list.txt phylosort filter --include-file pass_list.txt trees/*.nwk -o passed_trees/ 

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6. Advanced tree filtering techniques

This section covers patterns and examples for sophisticated queries.

6.1. Monophyly tests
To retain trees where a set of taxa is monophyletic:

phylosort filter --monophyletic "GenusA_species1,GenusA_species2,GenusA_species3" trees/*.nwk -o monophyletic_trees/ 

Interpretation: keeps trees where the listed taxa form a single clade.

6.2. Sister-group queries
Keep trees where taxon X is sister to taxon Y or to any member of a set:

phylosort filter --sister "TaxonX" --to "TaxonY,TaxonZ" input.nwk -o sister_matches/ 

6.3. Topological distance and shape filters
Filter by tree balance, maximum patristic distance, or distance between two tips:

phylosort filter --max-patristic 1.5 --min-balance 0.2 trees/*.nwk -o topology_filtered/ 

6.4. Support-aware filtering
Exclude or flag clades with low support; require minimum bootstrap or posterior probability for focal clades:

phylosort filter --require-support "Homo_sapiens,Pan_troglodytes:0.8" trees/*.nwk -o high_support/ 

This requires the clade containing those taxa to have support >= 0.8.

6.5. Regex and label mapping
Often input labels include species and gene IDs. Use regex to map or normalize labels before filtering:

phylosort normalize --regex "^(.*?)|.*$" --replace "\1" trees/*.nwk -o normalized/ phylosort filter --require "Homo_sapiens,Pan_troglodytes" normalized/*.nwk -o filtered/ 

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7. Performance and scalability tips

• Parallelize batch jobs with GNU parallel or xargs:

  
  ls trees/*.nwk | parallel -j 8 phylosort filter --require "Homo_sapiens" {} -o filtered/{/} 

• Pre-index or summarize trees with phylosort stats to avoid repeated parsing.
• Use memory-friendly options (streaming mode) when processing thousands of large trees.
• Use label hashing or numeric IDs to speed up repeated comparisons.

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8. Troubleshooting and best practices

• If trees have inconsistent label formats, normalize labels first.
• Check for unsupported Newick features (comments, edge annotations) — strip or convert them.
• Validate trees with phylogenetic libraries (e.g., ETE3, DendroPy) if parsing errors occur.
• When results seem off, run phylosort on a small subset and inspect outputs manually.

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9. Example pipelines

9.1. Full gene-tree filtering and species-tree input for concatenation

# 1. Normalize labels phylosort normalize --regex "^(.*?)|.*$" --replace "\1" raw_trees/*.nwk -o normalized/ # 2. Keep trees containing target species and min taxa phylosort stats normalized/*.nwk --min-taxa 8 --require "Homo_sapiens,Mus_musculus" -o pass_list.txt phylosort filter --include-file pass_list.txt normalized/*.nwk -o passed_trees/ # 3. Extract alignments corresponding to passed trees and concatenate (external step) # (Assumes mapping file from tree files to alignment files.) 

9.2. Detecting unexpected placements (HGT candidates)

phylosort filter --non-monophyletic "ExpectedCladeTaxaList" trees/*.nwk -o hgt_candidates/ 

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10. References and further reading

• Tree formats: Newick and Nexus specifications
• Phylogenetic Python libraries: Biopython, DendroPy, ETE Toolkit
• Best practices in phylogenomics (papers and reviews)

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If you want, I can:

• Provide a ready-to-run example dataset and commands tailored to your tree files, or
• Convert one of the example pipelines into a reproducible Snakemake or Nextflow workflow.