-fixed/modified the branch lengths in the RAxML_laballed tree output of the EPA
algorithm, now all branch lengths (both for queries and on the reference tree)
will be correctly displayed.
-added the ability to parse and display again trees with branch lengths for parsimony-based short read alignment
-made the joint json fromat compliant with the version 2 definition of the format
added RAxML_labelledtree format that includes placed query sequences to parsimony-based placement algorithm
extended RAxML's capability to read in pre-computed binary model parameter files as produced
by the -f e option for the following options:

1. standard tree search
2. per-site log likelihood calculation for a bunch of trees (-f g option)
3. log-likelihood evaluation of a bunch of trees (-f n option)

also added an example script for the read analyses called pavlatoras.pl
-fixed bug in ancestral states computations that only occured with codon-style partition files of type:
 DNA,	 part_1_codon1 = 1-60\3
 DNA,	 part_1_codon2 = 2-60\3
 DNA,	 part_1_codon3 = 3-60\3

The problem was that pattern compression for ancestral states was disabled to print out the ancestral states in correspondance to the sites
of the input alignment (without pattern compression and re-ordering). The problem is that when we disable pattern compression the code expects
sites belonging to the same model/partition to be stored contiguously in memory which under this codon scheme is not done if site compression is disabled.

In general we need to be very careful with partitioned models with non-contiguous sites and site compression disabled.

Kassian, this may also be relevant to the stuff you wanted to test.

I now integrated site compression into ancestral state computations and then bring the sites back into the original order once they are printed out to file.
I hope that I did not screw up the indices, initial tests suggest that it is correct though. To quote Derrick Zwickl, this is the most difficult part of implementing ancestral states.
- hopefully fixed the repeatedly faling assertions in evaluateGenericSpecial.c
fixed a bug that ocurred for the following parameter combination:

raxmlHPC -m PROTCATLGF -k -n test -s AAsmall.phy -x 95 -N 20 -p 22

the problematic combination was -k with -x and CAT
-fixed bug in fast tree search -f E
-added define _ALL_ENTRIES to print out all placements for each read
-included basic compile instructions in README
-added a more verbose parsing error message for secondary structure files
- added and updated ProteinModelSelection.pl script for selecting the best-scoring protein substitution model
  on a fixed parsimony tree.
little fix
-included model parameter count for AIC tests (only printed when -f e is used) for all models in RAxML
-added siwtch -O that allows for disabling the checking and error exit for completely undetermined sequences
-Now, the ProteinModelSelection.pl perl script will also work if some partitions have undetermined taxa, for
 model parameter estimation this shouldn't pose a problem
-added option -u that allows for using the median to approximate the GAMMA distribution
-added an error check that does not allow users to use the outgroup option in conjunction with
 ancestral state reconstruction. The input tree for ancestral state reconstructions must be rooted
 anyway, hence there is no use in specifying an outgroup and I don't know which effects this will have.
-added a more verbose error message to the partition parsing routine, it will now provide
 some info if users use / instead of \ for writing, e.g., DNA, p1=1-100\3.
-added command line switch -V to allow for using models without any correction for rate heterogeneity,
 only works if used in conjunction with the CAT approximation of rate heterogeneity that needs to be specified
 via -m as usual.
-fixed a nasty bug introduced by the rate scaling procedure for CAT (that will scale
 rate categories such that the man subst. rate is 1.0) that occured now and then
 when using the rapid bootstrapping procedure and made the following assertion fail:
 optimizeModel.c:2054: updatePerSiteRates: Assertion
`(((1.0 - accRat)<0) ? (-(1.0 - accRat)) : (1.0 - accRat)) < 1.0E-5'
failed