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.