- mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
- mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
- mothurOut("The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n");
- mothurOut("The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n");
- mothurOut("The phylotype command should be in the following format: \n");
- mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
- mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
+ m->mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
+ m->mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
+ m->mothurOut("The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n");
+ m->mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
+ m->mothurOut("For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n");
+ m->mothurOut("The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n");
+ m->mothurOut("For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n");
+ m->mothurOut("The phylotype command should be in the following format: \n");
+ m->mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
+ m->mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");