CladoCode: automated homogeneous subset analysis for cladistics

CladoCode

Automated homogeneous subset analysis for cladistics

Upload a data file

CladoCode is an online implementation of homogeneous subset coding described by Simon (1983). This method represents a repeatable, non-arbitrary method of coding metric data for phylogenetic analysis (Rae, 1998).

The program tests for homogeneous variances between samples, runs the appropriate multiple comparisons test, creates homogeneous subsets, then provides alphanumeric codes for each taxon for each variable. The coded data matrix and the accompanying statistical results are displayed on a webpage that can be saved on the local computer. If this is your first time using CladoCode, please read the file format information below before proceeding.

File format

To use the utility, you must provide a plain-text data file with space-separated or tab-separated columns. Most spreadsheet and database programs provide this as an option under File > Save as.... An example file is linked here.

The input file format is crucial — the program returns a blank screen if it is not formatted correctly. Check your text file after export to see that it conforms to the following key elements before you attempt to upload it:

The first column must be the names of the taxa. Any block of whitespace will be treated as a column delimiter, so avoid spaces in the names: use an underscore or CamelCase convention instead. Also avoid use of reference schemes such as "Taxon_cf." or "Group_spp." — these will be treated not as references, but as defining a new taxon with that exact name.
The first row must include a descriptor of the first column (e.g., "Taxa", or "Species", or "Populations"), then descriptors of the traits (e.g., "Trait1", or "femur_length", or "BMI"), each separated by any non-zero amount of whitespace.
All further rows represent individuals, with the taxon name and the data points all separated by whitespace. You can use multiple spaces or tabs to visually align columns if you like.
Every line must end with a carriage return.
There must be no missing data — more whitespace does not indicate a missing column, and any row without enough entries will result in a blank screen. You will need to separate your data set into multiple input files if data are missing for any individuals.

It is assumed that the data are properly scaled, so as to reduce the influence of size (Rae, 2002).

Code

The code of this utility is available as a Python module and scripts for command-line and web-based use: download package as zip file.

Citation

If you use the utility, please cite the following:

Rae, T., Buckley, A., CladoCode, 2009, arXiv:1411.4550 [stat.AP]
https://arxiv.org/abs/1411.4550

References

Rae, T., 1998. The logical basis for the use of continuous characters in phylogenetic systematics. Cladistics 14(3), 221-228.
Rae, T., 2002. Scaling, polymorphism, and cladistic analysis. In: Forey, P., MacLeod, N. (Eds.), Morphology, Shape & Phylogenetics. Taylor & Francis, London, pp. 45-52.
Simon, C., 1983. A new coding procedure for morphometric data with an example from periodical cicada wing veins. In: Felsenstein, J. (Ed.), Numerical taxonomy. Springer-Verlag, Berlin, pp. 378-382.