-fixed bug in ELW computation (-f w and -f W options)
-little bug fix for computation of sh-like support values
-small modification to IC and TC computation
-completely removed the multi-threaded lockless allocator from all Pthreads and HYBRID Makefiles
 because of recurrent performance and compiling problems.
-improved (almost final version) of IC and TC score calculations according to Rokas and Salichos 2013
-included TC-All and IC-All metrics that take all conflicting bipartitions with support > 5% into account
 when calculating the TC and IC scores
-The output trees are annnotated by IC and IC-All scores that are displayed as branch labels in standard Newick format,
 that is lables such as [x,y] where x is the IC score and y is the IC-All score
-added flag -C that will generate verbose output for IC and TC calculations
	-it will print the support for each bipartition and
         all conflicting bipartitions to the RAxML_info file
        -it will generate files called RAxML_verboseIC.RUN_ID.N
         that for each bipartition in the tree from 1...N contain the
         bipartition that was included into the tree as well as all conflicting
         bipartitions with >5% in Newick format
-added an algorithm for rooting trees. It will root the tree at the branch that best balances the subtree lengths (patrsitic distances)
 of the two subtrees defined by this branch.
 example: ./raxmlHPC -f I -t smallTree5 -m GTRCAT -n runID
-refined the TC and IC calculations Salichos and Rokas (2013)
-integrated Andre's patch for generating bootstrap replicates
updated version number
-cleaned up the implementation of the population count in the parsimony functions
-updated version number and date
further cosmetic changes to popoluation count
-changed implementation of rax_malloc to call posix_memalign() by default in order to avoid
 potential bugs with AVX and SSE3 versions
-note that there is probably no way to have a memory-aligned realloc() without keeping track
 of the length of the pointer to be reallocated in the application code
-fixed some minor compiler issues with the Makefiles and source files
-updated version number
-fixed a bug in the Q-rate matrix optimization for secondary structure models
 and updated the version number
Updated version numbers
-added even more verbose PHYLIP-like formatted output for supported and conflicting bipartitions
 for the IC and TC score calculation from Rokas and Salichos 2013. Note that, the verbose output
 for all IC and TC-related calculations is activated by -C
-fixed a bug in the model parameter optimization routine
-added an option -X that will execute a randomized addition order parsimony tree
 building algorithm and then exit (as opposed to -y) without doing any parsimony-based SPRs.
 This is helful for generating more diverse (topologically different) parsimony-based starting tree
 on whole-genome alignemnts that often show a very clear signal for one or just a few parsimony trees.
-fixed a small issue in the fasta file parser that occured with Windows line breaks
Added some functions to handle multi-furcating trees for the tree plausibility checker option.
These functions can be activated by undefining: _ONLY_BIFURCATING_TREES in bipartitionList.c.
Those are experimental functions, so don't fiddle around with them if you don't know what you are doing!
added some more comments to the code in bipartitionList.c
fixed a small bug in the tree rooting algorithm (the new -f I option)
-added the ability to parse trees with branch-labels (not node labels) as displayed
 in the RAxML_bipartitionsBranchLabels.RUN_ID files in the tree rooting option (-f I option)
 and display them on the rooted tree.
 Note that, the branch label (representing the support) at the root will be duplicated,
 that is, if I insert the root at an inner branch with a support of say 68, a branch label
 with support 68 will be displayed on each of the two branches descending from the root.
updated version numbers