The MLgsc programs and their functions, inputs, and outputs.

(a) A multiple alignment provided by the user of known sequences from the gene or protein of interest, in Fasta format. (b) A phylogeny of the reference taxa provided by the user in Newick format. (c) A text output, containing (among others) the actual and predicted taxon names, thus enabling the detection of classification errors. (d) This step is conditioned on a successful cross-validation (mlgsc_xval). (e) This is a binary file, to save space and to save reading and parsing time (f) A Fasta file containing the sequences to be classified, usually unaligned. (g) The output of mlgsc_train. (h) A text file that contains the predicted assignment to reference taxa for each query sequence (among other information). The MLgsc programs and their functions, inputs, and outputs.