Agalma

Agalma automates construction of gene sequence matrices and preliminary species trees from raw Illumina transcriptome data and public genomes and transcriptomes to support phylogenomic analyses.

Key Features:

• Automated Workflow: Automates construction of gene sequence matrices and preliminary species trees from raw Illumina transcriptome data, enhancing reproducibility and efficiency.
• Integration with Diverse Data Sources: Incorporates sequences from newly sequenced transcriptomes and publicly available genomes and transcriptomes.
• Comprehensive Diagnostics and Reporting: Provides detailed diagnostics at each analysis stage and generates HTML reports documenting processor and memory usage, metadata management, and version control of external programs.
• Built on BioLite Framework: Uses the BioLite framework to track provenance, profile computational resources, and comprehensively log analytical steps to support reproducibility.
• Modular Workflow for Method Development: Employs a modular design that allows optimization of individual components within a full phylogenomic analysis and includes bundled test data.

Scientific Applications:

• Large-scale phylogenetic inference: Enables construction of comprehensive phylogenies from hundreds to thousands of genes across diverse taxa.
• Evolutionary biology and systematics: Supports analyses of species relationships and evolutionary histories using combined transcriptome and genome data.

Methodology:

Data input: raw Illumina transcriptome data; Annotation and assembly: annotate assemblies and align gene sequences into matrices; Phylogeny construction: generate a preliminary species tree from aligned sequences; Diagnostics and reporting: provide detailed diagnostics and generate comprehensive HTML reports documenting processor and memory usage, metadata management, and external program version control.