Evolutionary Analysis Results

Nature: Analysis results derived from DNA sequence data, including phylogenetic analyses, networks, biogeography reconstruction., ancestral character state reconstructions, and more. Includes all files related to an analysis, such as matrices, command blocks, scripts, analysis logfiles and outputs, phylogenetic trees, networks and documentation of each analysis.

File formats: Includes various formats provided by analysis software.

Storage / folder organization:

- Subfolder for analysis results: Store all analysis results in a dedicated subfolder within the relevant project folder.

Organize by datasets: Each dataset should have its folder within the analysis results folder.

Subfolders for each analysis: Create subfolders for each individual analysis, clearly labelled with the date and the analysis method. These subfolders should contain all files related to that specific analysis, like matrices, command files or blocks, log files and resulting trees. Include any further relevant information into a README file.

Tree visualizations: Store any tree visualizations alongside the corresponding analysis data.

Example folder structure

Dianthus_phylogeny [project folder]

└── Phylogenetic_analyses

└── ITS

└── 2024-01-15_MaximumLikelihood

└── 2024-01-20_BayesianInference

└── trnK-matK

└── 2024-02-10_ MaximumLikelihood

└── 2024-02-11_ BayesianInference

Naming convention: Use short and descriptive file names to reflect the content. The analysis type and the data can also be included in the file name.

Examples:

Jurinea_ITS_datasetC.nex

Arenaria_ITS_120taxa.nex

Dianthus_trnKmatK_2024-01-15.nex

Dianthus_ITS_2024-01-15_BI.nex

Link to source data: Ensure that matrices and analysis outputs are clearly linked by maintaining consistent file names.

Jurinea_ITS_datasetC.nex [matrix]

Jurinea_ITS_datasetC.con [tree]

Version control: Include dates in the file names to track different versions of the matrices or analyses.

Example:

Pyrus_plastid_combined_2017-04-05.nex

Metadata: Document analysis parameters, software, version and any other relevant parameters or notes not included in the analysis logfiles. Store in README files for each analysis.

Retention: As logfiles tend to be large, retain only latest analyses, unless earlier versions are needed. At the end of the project, retain only the final published version.

Publication:

• Publish trees in *.nex format along with the manuscript or upload to a repository
• Store final/published version of the analyses, matrices, command files, trees files and any other relevant files along with the manuscript files, ensuring the to the publication is maintained.