- m->mothurOut("The cluster.split command parameter options are phylip, column, name, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, large, processors. Phylip or column and name are required.\n");
+ m->mothurOut("The cluster.split command parameter options are fasta, phylip, column, name, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, large, processors. Fasta or Phylip or column and name are required.\n");
+ m->mothurOut("The cluster.split command can split your files in 3 ways. Splitting by distance file, by classification, or by classification also using a fasta file. \n");
+ m->mothurOut("For the distance file method, you need only provide your distance file and mothur will split the file into distinct groups. \n");
+ m->mothurOut("For the classification method, you need to provide your distance file and taxonomy file, and set the splitmethod to classify. \n");
+ m->mothurOut("You will also need to set the taxlevel you want to split by. mothur will split the sequence into distinct taxonomy groups, and split the distance file based on those groups. \n");
+ m->mothurOut("For the classification method using a fasta file, you need to provide your fasta file and taxonomy file. \n");
+ m->mothurOut("You will also need to set the taxlevel you want to split by. mothur will split the sequence into distinct taxonomy groups, and create distance files for each grouping. \n");