MACER

MACER assembles taxonomically and marker-focused molecular sequence datasets from online repositories (including NCBI GenBank) as an R package to support dataset curation for genomics, phylogenetics, and evolutionary biology.

Key Features:

• R package implementation: Implemented as an R package to script and reproduce dataset assembly workflows.
• Data Assembly: Automated acquisition, accumulation, and organization of sequence data from online molecular repositories.
• Dereplication: Identification and removal of redundant or duplicate sequence entries to maintain dataset integrity.
• Cleaning: Processing of datasets to remove inconsistencies and prepare sequences for downstream analysis.
• Customization for specific applications: Construction of taxonomically and marker-targeted datasets based on user-defined criteria.

Scientific Applications:

• Genomics: Curation of sequence datasets for comparative and marker-based genomic analyses.
• Phylogenetics: Assembly of marker-specific and taxonomically focused sequence sets for phylogenetic inference.
• Evolutionary biology: Preparation of cleaned, non-redundant sequence datasets to support evolutionary analyses.
• Comparative studies: Generation of consistent datasets across projects to enable comparative molecular studies.

Methodology:

Automated access to online molecular sequence repositories (e.g., NCBI GenBank); targeted searching and downloading of sequences based on user-defined criteria; dereplication to remove duplicate sequences; and dataset cleaning to remove inconsistencies and prepare sequences for analysis.