PhySpeTree

PhySpeTree reconstructs phylogenetic species trees for bacterial, archaeal, and eukaryotic organisms by automating genomic data retrieval, sequence cleaning, and complementary concatenated conserved-protein and small subunit ribosomal RNA–based inference for evolutionary analyses.

Key Features:

• Automated configuration: Prepares configuration files to integrate multiple software tools used in phylogenetic workflows.
• Automated data handling: Downloads genomic data and performs sequence cleaning for downstream analysis.
• Dual reconstruction pipelines: Provides a pipeline based on concatenated highly conserved proteins and a pipeline using small subunit ribosomal RNA sequences.
• Advanced customization: Exposes adjustable options for sequence alignment and tree construction steps.
• Accessory modules: Supports insertion of new species into existing datasets, generation of visualization configurations, and combination of multiple trees.
• Implementation: Implemented in Python.

Scientific Applications:

• Species tree reconstruction: Infer species relationships across bacterial, archaeal, and eukaryotic taxa using concatenated protein or small subunit ribosomal RNA data.
• Comparative evolutionary analyses: Analyze large-scale genomic datasets to compare phylogenetic hypotheses, combine multiple trees, and integrate new taxa for evolutionary pattern inference.

Methodology:

Automatic download of genomic data, sequence cleaning, preparation of configuration files to integrate multiple software tools, two parallel pipelines using concatenated highly conserved proteins and small subunit ribosomal RNA sequences, configurable sequence alignment and tree construction steps, and modules for insertion of new species, generation of visualization configurations, and combination of multiple trees.