Coseg - 0.2.4

• IUB codes in input sequences caused the code to segfault.
  Coseg will now randomly choose a nucleotide to substitute
  each time it encounters one in in the input sequence. It
  will also inform the user when doing so. Thanks to David
  Ray for reporting this and suggesting the fix.
• Fixed the svg tag so that the files
  will directly load in HTML5 web browsers.
• Calculation of divergence has been improved.
  We now use kimura substition distance with CpG
  site accounting modifications instead of the
  mixed substition and indel calculation.
• Produce a warning if emutfrac is not within expected
  range, rather than crashing.

Coseg 0.2.3

Fix to the Makefile to make it easier to compile on modern toolchains.

Coseg - 0.2.2

• Create a *.svg graph file without the need
  to download/use GraphViz. The layout is
  handled by an adaptation of algorithm
  developed by Atze van der Ploeg. The SVG
  file produced supports various labeling
  options and subfamily details displayed
  when a node is hovered over.
• Changed the default colormap for the graph
  output. Now warm colors denote more diverged
  subfamilies in the tree while cooler colors
  represent younger subfamilies. To restore
  the original color scheme use the new "-o"
  flag to coseg.
• Added parameter to control the minimum distance
  between diagnostic sites. Now the user can override
  the historic value of 10 using the -u flag.
• Improved error reporting when there is a mismatch
  between an individual sequence length and the
  consensus length in the input files.
• Fixed a bug that caused coseg to segfault.
• Added experimental script refineConsSeqs.pl. This
  script uses the RepeatModeler application to build
  and refine the consensus sequences for each
  subfamily.