topiary

topiary reconstructs ancestral amino acid sequences and associated phylogenetic relationships to infer evolutionary histories of protein families through ancestral sequence reconstruction (ASR).

Key Features:

• Automated taxonomic scope determination: Infers taxonomic scope and identifies relevant sequences using BLAST.
• Sequence quality control and redundancy reduction: Performs taxonomically informed quality control and reduces redundancy among input sequences.
• Multiple sequence alignment: Constructs multiple sequence alignments using Muscle5.
• Gene tree construction: Builds gene trees with maximum-likelihood methods using RAxML-NG.
• Species tree reconciliation: Reconciles gene trees with species trees using GeneRax and PastML.
• Ancestral sequence reconstruction: Reconstructs ancestral amino acid sequences from reconciled phylogenies.
• Branch support determination: Assesses statistical support for phylogenetic branches.
• Comprehensive outputs: Produces annotated evolutionary trees, spreadsheets with sequence data, and graphical summaries evaluating ancestor quality.

Scientific Applications:

• Protein evolutionary inference: Infers ancestral protein sequences and gene trees to study evolutionary relationships among protein sequences, structures, and functions.
• Functional and adaptive evolution studies: Enables investigation of historical amino acid changes underlying functional innovations and adaptive shifts in protein families.

Methodology:

Uses BLAST for sequence identification and taxonomic scope inference; Muscle5 for multiple sequence alignment; RAxML-NG (maximum-likelihood) for gene tree construction; GeneRax and PastML for reconciliation processes and ancestral inference; and references NCBI and the Open Tree of Life for sequence and species-tree data.