phylotaR

phylotaR retrieves orthologous DNA sequences from GenBank for use in phylogenetic inference.

Key Features:

• Ortholog Identification: Uses alignment searches to identify orthologous sequences and mitigate sequence mislabeling and incorrect species identification.
• Modular Pipeline: Implements a modular pipeline building on PhyLoTa for flexible processing of large datasets.
• Handling Data Complexity: Processes large and complex GenBank datasets to select relevant orthologous sequences.
• Improved Accuracy: Reduces noise, error, and bias in phylogenetic inference by focusing on orthologs and using up-to-date GenBank data.
• Versatility Across Taxa: Applied to large taxonomic clades such as Palms and Primates, demonstrating cross-taxa utility.

Scientific Applications:

• Phylogenetic reconstruction: Assembles orthology-aware sequence datasets from GenBank for phylogenetic tree inference.
• Error reduction in evolutionary analyses: Minimizes impacts of sequence mislabeling and paralogy on downstream evolutionary and comparative studies.
• Large-scale taxonomic analyses: Enables analyses across diverse and large taxonomic clades using comprehensive GenBank sequence data.

Methodology:

Accesses GenBank to retrieve DNA sequences, employs alignment searches to identify orthologous sequences, and identifies overlapping sequence clusters.