New function Rdnamlk

Uses Rdnaml and dnamlk (which enforces molecular clock) internally.
Fix to Rdnaml for clock=TRUE

Remove options speedier and outgroup if clock==TRUE.
New internals; working on Rthreshml.
Working Rthreshml, without parsing outfile.
Minor changes to Rthresml

Still working on this. Have not finished code to parse in outfile.
Rthreshml with outfile parsed back in.
Started working on Rtreedist
Finished Rtreedist.

Still testing.
New man pages & other updates. New build.
New function Rdnadist.
More on Rdnadist

Fixes & updates to Rdnadist. Now returns object of class "dist" instead
of matrix. Man page for Rdnadist.
New fn Rdnapenny.

New fn Rdnapenny. New man page. New Rphylip build.
New fn Rconsense
Started working on Rproml/Rpromlk
...

Rproml seems to work; Rpromlk does not. Also addt'l fns for reading
protein sequences and a S3 print method for the object created by
read.protein.
New functions to handle aa sequences

New functions for protein sequences. Some other stuff.
Documentation & new build
...
sim.code
Some work on .Rd files.