read_input: Called by create_job to read input files
In pastis: Phylogenetic Assembly with Soft Taxonomic Inferences

Reads the specified input files and performs some basic consistency checking between the inputs.

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  read_input(constraint_tree, taxa_list,
    missing_clades = NA, sequences = NA,
    output_template = NA)

`constraint_tree`	A tree with constraints that are forced to be present in all output trees. Either a filename to a nexus file readable by read.tree or a ape phylo object.
`taxa_list`	A list of all taxa and their clades. Either a data frame with columns "taxa" and "clade" or a filename for a file readable by read.csv with those columns
`missing_clades`	A file containing missing clades. Each line of the missing clades file consists of the missing clade, the word "include" or "exclude" and a list of the reference clades (all separated by commas). Lines containing "include" specify that a taxon is contained below the MRCA of the reference clades. Lines containing "exclude" specify that the missing clade cannot attach below the MRCA of the reference clades. #'
`output_template`	The filename for a template for the output nexus file. This file should look like a regular mrBayes input file with special tags replacing content that will be filled by pastis. In particular: <sequences> will be replaced by the sequences (and should go below the MATRIX line) <ntax> the number of taxa (i.e. "ntax=<ntax>" must be somewhere in your template) <nchar> the number of characters <constraints> the constraints will go here <outputfile> where the summaries will be written, (i.e. `"sumt filename=<outputfile> burnin ...."` should be in your template) see default_output_template for an example (which is used by default)
`sequences`	A file with all the available sequence information in fasta format for details on that format see read.dna in the ape package.