modified info messages
modified kmean_wrapper() and ss()

* Neither function worked with the new likelihood lists (already as a
log likelihood) or the new call to processor. Modified to work with
both.
changed log.info to log.error for errors
modified call to starting tree

* Modified the call so that it doesn't use any slashes (OS specific),
and that it will call the correct starting tree (used to call
topology_tree.phy, there are other trees with branch lengths for eiter
phyml or raxml, which can be called by making topology)
modified new make_tree_path() function

* old function (still in file, but commented out) called
RAxML_result.BLTREE from the phylofiles folder when the tree is stored
in the starting_tree folder. New functions returns correct alignment
path.