agalma 1.0.0

An automated phylogenomics pipeline.

Agalma is an automated tool that constructs matrices for

phylogenomic analyses, allowing complex phylogenomic analyses to be implemented and described unambiguously as a series of high-level commands. The user provides raw Illumina transcriptome data, and Agalma produces annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics that allow the investigator to make extensive assessments of intermediate analysis steps and the final results. Sequences from other sources, such as externally assembled genomes and transcriptomes, can also be incorporated in the analyses. Agalma is built on the BioLite bioinformatics framework, which tracks provenance, profiles processor and memory use, records diagnostics, manages metadata, installs dependencies, logs version numbers and calls to external programs, and enables rich HTML reports for all stages of the analysis. Agalma includes a small test data set and a built-in test analysis of these data.