REALPHY

REALPHY constructs phylogenies from whole-genome sequencing data by mapping raw sequencing reads to multiple reference sequences to extract single nucleotide polymorphisms (SNPs) for phylogenetic inference.

Key Features:

• Phylogenetic Tree Inference: Automates inference of phylogenetic trees from sequence-derived variant data using SNP-based approaches.
• Reference Sequence Alignment: Maps raw sequencing reads to multiple reference genomes rather than relying on a single reference or on assembled/annotated genomes and orthologous gene alignments, thereby mitigating reference-associated biases and errors.
• SNP Extraction: Extracts single nucleotide polymorphisms (SNPs) from read-to-reference alignments for downstream phylogenetic analysis.
• Input Formats: Accepts genome sequence data in FASTA, GenBank, and FASTQ formats as input for read mapping and variant extraction.
• Comprehensive Output: Produces sequence alignments, phylogenetic tree files, and detailed information on SNPs and deleted sites for further analysis and validation.

Scientific Applications:

• Microbial evolutionary studies: Reconstructs phylogenetic relationships among microbial taxa from whole-genome sequencing data.
• Phylogenetic method evaluation: Enables assessment and comparison of phylogeny reconstruction accuracy, including analyses using simulated sequences to examine biases from single-reference approaches.

Methodology:

REALPHY maps raw sequencing reads to multiple reference genomes, extracts SNPs from the resulting alignments, and infers phylogenetic trees from those SNPs using maximum likelihood methods while avoiding genome assembly and ortholog alignment steps.