CVTree

CVTree infers phylogenetic relationships among microbial organisms by analyzing the oligopeptide composition of their complete proteomes using an alignment-free composition vector approach.

Key Features:

• Alignment-free composition vector (CV) method: Uses an alignment-free composition vector approach to reconstruct phylogenies without sequence alignment and without requiring 'free' parameters or fine-tuning.
• Proteome-based oligopeptide analysis: Analyzes oligopeptide composition of complete proteomes to derive composition vectors for comparative phylogenetic analysis.
• Comprehensive genome database: Includes over 850 prokaryotic genomes and more than 80 fungal genomes with monthly updates from NCBI and other sequencing centers.
• Versatile tree output options: Produces phylogenetic trees with options to collapse monophyletic branches at various taxonomic levels for comparative analysis of phylogeny and taxonomy.
• Standalone software with parallel workflow: Provides a standalone implementation with an extensible parallel workflow to support large-scale analyses.
• Support for diverse genome types: Applies to whole genomes, chloroplast genomes, mitochondrial genomes, and metagenomes.
• Broad taxonomic application and validation: Has been applied to viruses, prokaryotes, and fungi and validated by a bootstrap test of 139 organisms that supports the SSU rRNA tree of life.

Scientific Applications:

• Microbial genomics: Rapidly infers genome-scale phylogenetic relationships when proteome data are available.
• Evolutionary biology: Provides alignment-free phylogenetic reconstructions for studying evolutionary relationships across viruses, prokaryotes, and fungi.
• Taxonomy and classification: Offers an independent, whole-proteome-based method for verifying and comparing taxonomy derived from single-gene analyses such as SSU rRNA.

Methodology:

Computes composition vectors from oligopeptide composition of complete proteomes using an alignment-free CV approach, employs an extensible parallel workflow for computation, and applies bootstrap testing (reported for 139 organisms) for validation.