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debian/3.69.660-2

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Release 3.69 update July 2011

	Changed -thresh to -dothreshold and -gamma to -gammatype to avoid
	qualifier name clashes with stricter ACD validation.

	The *boot applications reported the status of some boolean options
	and printed "Done" at the end. Removed the boolean reports and now
	only print "Done" unless -noprogress is set to allow piping.

Release 3.69

	Updated all code to include the changes in phylip 3.69.

Release 3.68

	Updated all code to include the changes in phylip 3.68.
	fdnadist no longer writes a blank line at the end of the output.
	fconsense writes trees with 2 decimal places.
	A bug in fprotdist for scores of 100.0 is fixed.
	Rearrangement messages are no longer printed by fpromlk.
	fprotdist and fprotpars now write "Done" when completed.

	Renamed fdrawgram qualifiers to make unambiguous names shorter:
	xmarginray => xrayshade ymarginray => yrayshade for RayShade
	output image size in pixels.

	Removed unused fdrawtree qualifiers plotterpcl and plotterpcx.
	Added 4 new plotter options for the additional resolutions
	previously defined by plotterpcl and plotterpcx.
	Renamed fdrawtree qualifiers to make unambiguous names shorter:
	xmarginray => xrayshade; ymarginray => yrayshade for RayShade
	output image size in pixels.

Release 3.67

	Updated all code to phylip 3.67. The output of several programs has
	changed - see the phylip release notes for details. Programs with
	changed output are all the molecular clock algorithms : fcontml,
	fdnaml, fdnamlk, proml, promlk, restml. ftreedist and ftreedistpair
	branch score distance output has also changed in phylip 3.67

	fontfile now works correctly in fdrawgram and fdrawtree. The
	fontfile value must be a known phylip font in the data directory.

	previewing with X11 was broken. Setting "none" for previewer no
	longer prompts before plotting.

	frestdist had a memory access error reported by valgrind. The same
	error was found in the original phylip source, and fixed by
	copying in code changes in phylip 3.66

	fclique had an error reading the ancestors file. Results now agree
	with those from the original phylip 3.6 code.

	fdnamove had an internal overflow. Array chh[11] needed at least
	one extra space.