ADACT

ADACT computes alignment-free dissimilarities among nucleotide and protein sequences using Minimal Absent Words (MAW) and Relative Absent Words (RAW) to enable sequence comparison and phylogenetic analysis.

Key Features:

• Alignment-free analysis: Uses Minimal Absent Words (MAW) and Relative Absent Words (RAW) as core methods for sequence dissimilarity computation without alignment.
• Supported sequence types: Analyzes nucleotide and protein sequences and accepts multiple genome sequences as input.
• Configurable parameters: Allows specification of K-mer size, absent word type (MAW or RAW), dissimilarity index, and reverse complement setting (RC-setting).
• Distance outputs: Produces pairwise distance matrices quantifying dissimilarities between sequences.
• Species relationship outputs: Generates a sorted list of species relationships based on computed distances and infers phylogenetic trees using Neighbor Joining and UPGMA methods.

Scientific Applications:

• Evolutionary biology: Supports comparative analyses of species relationships and divergence using alignment-free dissimilarity measures.
• Genomics and comparative genomics: Facilitates large-scale sequence comparison and relationship inference across genomes and proteomes.
• Phylogenetic reconstruction: Provides distance-based inputs for Neighbor Joining and UPGMA tree construction to represent evolutionary relationships.

Methodology:

Computes Minimal Absent Words (MAW) and Relative Absent Words (RAW) of specified K-mer length, applies a dissimilarity index (with optional reverse-complement consideration), and derives pairwise distances between sequences without performing sequence alignments.