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Description:
agalma 1.0.0
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.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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