11-10-2010: 1.2 released 
	* added memory handler so that memory allocated in C is no longer
	  lost due to function interrupt (or failure to explicitly free it)
	* added support for alternate lineage-specific models within
	  the tree model object
	* added support for codon models (HKY_CODON, REV_CODON, SSREV_CODON),
	  also codon.clean.msa function
	* to support lineage-specific models, added support for labels in
	  phylogenetic trees which are denoted by the pound sign ie,
	  "((human #primate, chimp #primate)#primate, mouse)"
	* many changes to phyloFit; allow lineage-specific models, arbitrary
	  parameter boundaries, hold specified boundaries constant.  Some
	  of the default options are now different from command-line phyloFit.
	* added plot.msa and as.track.msa functions which plot alignment; only
	  currently works if alignment fits in the plotting window.  Also
	  added coord.range.msa function to support this.
	* added plot.rate.matrix (and plot.tm and plot.altmodel.tm)
	* added set.rate.matrix.tm and get.rate.matrix.params.tm which set 
	  a rate matrix based on substitution model parameters, or get the 
	  substitution model parameters describing a rate matrix, respectively.
	* added summary.tree function which returns a data frame with various
	  information about each branch
	* fixed bug in split.by.feature.msa in which offset of resulting msas
	  was one higher than it should have been
	* changed several function names to increase consistency in naming 
	  conventions:
	    addUTRs.feat -> add.UTRs.feat
	    addIntrons.feat -> add.introns.feat
	    addSignals.feat -> add.signals.feat
	    fixStartStop.feat -> fix.start.stop.feat
	    validFormatStr.msa -> is.format.msa
	    isSubstMod.tm -> is.subst.mod.tm
	    branchlen.tree -> branchlength.tree
	    wig.track -> as.track.wig
	    feat.track -> as.track.feat
	    gene.track -> as.track.feat(is.gene=TRUE)
	* added pairwise.diff.msa function which returns pairwise differences
	  per site between pairs of sequences in an alignment
	* fixed some minor bugs in documentation (multiple notes in functions,
	  help("[.msa") not working previously)
	* Switched order of arguments in write.feat to (feature, file) for 
	  consistency with all other write functions.
	* added functions postprob.msa, expected.subs.msa, and 
	  total.expected.subs.msa
	* allow ref.idx argument in phyloP to refer to features object
	* removed region.bounds argument from coverage.feat; now requires at 
	  least one features object have not=FALSE

2010-09-17: 1.1 released
	* updated DESCRIPTION
	* updates to Makevars and configure.ac to resolve error compiling 
          on Solaris
	* fixed bug causing segmentation fault in gff.c

2010-09-15: 1.0 released
