Phylosift

Phylosift performs phylogenetic analysis of genomic and metagenomic DNA sequences to infer evolutionary relationships and detect organisms within microbial communities.

Key Features:

• Phylogeny-Driven Bayesian Hypothesis Testing: Uses Bayesian statistics to test for the presence of specific organisms in samples based on phylogenetic data.
• Community Structure Comparison: Compares microbial community structures across multiple samples and associates abundance patterns with sample metadata.
• Phylogenetic Diversity Analysis: Analyzes phylogenetic diversity within microbial communities to relate community composition to sample-specific factors.
• Integration with LAST, HMMER, and pplacer: Integrates LAST for sequence alignment, HMMER for protein domain searches, and pplacer for phylogenetic placement on protein-coding and RNA sequences.
• Support for Illumina and 454 data: Processes sequence data derived from Illumina and 454 sequencing platforms.

Scientific Applications:

• Environmental microbial ecology: Investigating environmental and uncultured microbial communities and their evolution using metagenomic data.
• Forensic and pathogen detection: Detecting pathogens in forensic or clinical samples and providing phylogenetic evidence for organismal presence.
• Ecological and evolutionary hypothesis testing: Linking phylogenetic profiles with sample metadata to identify correlations between organism abundance and environmental or experimental conditions.

Methodology:

Scans sequence data against a reference database of protein sequences to identify homologs, uses LAST for sequence alignment, HMMER for protein domain searches, and pplacer for phylogenetic placement, constructs phylogenetic relationships between new sequences and database entries, and applies phylogeny-driven Bayesian hypothesis testing to infer organism presence.