agalma

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.