PROP

PROP incorporates evolutionary models that account for gaps (insertions and deletions) in sequence alignments to estimate genetic differences and construct phylogenetic trees.

Key Features:

• Incorporation of Gap Sites: Includes information from gap-containing sites (insertions and deletions) in sequence alignments when estimating genetic differences.
• Distinctive Genetic Difference Estimation: Retains gap sites in calculations to enable detection of evolutionary differences that can alter phylogenetic tree topologies compared to analyses that exclude gaps.

Scientific Applications:

• Comprehensive phylogenetic inference: Enables phylogenetic analyses that require inclusion of insertion/deletion information to represent a fuller spectrum of genetic variation.
• p53 sequence analysis: Demonstrated on complete p53 amino acid sequences from 31 organisms, producing phylogenetic trees that differ significantly when gap information is included versus excluded.

Methodology:

Implements a novel genetic-difference measure that incorporates evolutionary information from aligned and gap-containing (insertion/deletion) sites and uses that measure to compute genetic distances for phylogenetic tree construction.