Changes throughout code, both to further develop the capabilities of the software and in response to tester feedback. At this point, the API should be basically set for release. Major new functionality:
Tree drawing now incorporated into topiary
Inference steps now take output directories from previous runs as inputs. This facilitates creation of pipelines and minimizes error if a user (for example) mistakenly uses a different model for different steps in the pipeline.
Cleaned up and standardized the raxml, generax, and muscle interfaces.
Added more unit tests. (Significant coverage gaps remain).
Changes throughout code, both to further develop the capabilities of the software and in response to tester feedback. At this point, the API should be basically set for release. Major new functionality: