		CHANGES IN PEGAS VERSION 0.3


NEW FEATURES

    o The new function edit.loci allows to edit allelic data frame while
      keeping the attributes correct (which edit.data.frame doesn't).

    o There are new rbind() and cbind() methods for objects of class
      "loci".

    o There is a print 'method' for the class "haplotype".

    o `[.loci` has now an option 'drop = TRUE'.

    o There is a vignette detailing how to read allelic data files of
      various formats into R: type vignette("ReadingFiles") in R.


BUG FIXES

    o amova() did not compute SSD correctly with a single level.

    o getAlleles() did not work correctly.

    o read.loci() did not work when `col.pop' was used.

    o Checking for ordered alleles did not work (i.e, A/a and a/A were
      treated as different genotypes: they are now pooled).

    o The display of haplotype labels by plot.haploNet() was not
      effective.


OTHER CHANGES

    o read.loci() loses the `skip' option which is replaced by `...'.



		CHANGES IN PEGAS VERSION 0.2


NEW FEATURES

    o The new function site.spectrum computes the (un)folded site
      frequency spectrum of a set of DNA sequences.

    o The new function theta.tree estimates THETA from a phylogenetic tree
      under a simple coalescent model by maximum likelihood.

    o There is now a "[" method for the class "loci".

    o haplotype() has now an option 'labels' to give as rownames of
      the returned object.

    o amova() has a new option 'is.squared' to specify whether the
      distance matrix has been squared beforefand (FALSE by default).

    o write.loci() has a new argument '...' passed to write.table().

    o The functions heterozygosity, nuc.div, theta.h, theta.k and
      theta.s have been moved from ape to pegas.


BUG FIXES

    o amova() did not compute SSD correctly.

    o summary.loci() failed in the presence of NA's.
