webPRANK

webPRANK performs phylogeny-aware multiple sequence alignment to integrate evolutionary models into alignments for accurate comparison of DNA, protein and codon sequences and to support selection inference and ancestral-sequence reconstruction.

Key Features:

• Phylogeny-Aware Progressive Alignment: Implements a phylogeny-aware progressive alignment algorithm that integrates evolutionary models and provides posterior probabilities for sequence sites either concurrently with alignment or as a post-processing step.
• Sequence Type Support: Supports DNA, protein, and codon sequences, including protein-translated alignment of cDNAs and built-in structure models for genomic sequence alignment.
• Alignment Reliability Filtering: Provides post-processing to remove alignment columns with low posterior reliability in the context of a cladogram.
• Export Formats: Exports resulting alignments in formats commonly used for evolutionary sequence analyses.
• Ancestral Sequence Inference: Infers ancestral sequences with phylogenetically realistic gap patterns.
• Annotation and Post-Processing: Supports annotation and post-processing of existing alignments.

Scientific Applications:

• Inference of Selection on Codon Sequences: Enables inference of selection on codon sequences by producing codon-aware alignments with phylogenetic context.
• Molecular Evolution and Evolutionary Modeling: Facilitates studies of molecular evolution and modeling of complex evolutionary processes through phylogeny-aware alignments.
• Ancestral Genome Reconstruction: Aids reconstruction of ancestral sequences and investigation of lineage-specific adaptations using inferred ancestral sequences with realistic gap patterns.
• Preparation for Downstream Phylogenetic Analyses: Produces alignments and site-reliability assessments suitable for downstream phylogenetic inference and comparative sequence analyses.

Methodology:

Uses phylogeny-aware progressive alignment that integrates evolutionary models into the alignment process, computes posterior probabilities for sequence sites (concurrently or post-processing), supports protein-translated cDNA alignment and built‑in genomic structure models, performs ancestral-sequence inference with phylogenetically realistic gap patterns, and allows removal of low-posterior-reliability columns as post-processing.