2012-11-14 Release 1.1.0

	New application eomegaps to align a profile (aligned sequences)
	to a single sequence. Only the profile-profile input is allowed
	for this case by clustalo.

	Renamed inputs and outputs with 'file' at the end. note 'profile'
	happens to already end with the required characters.

	Added -outformat option to select the format generated by clustalo
	for the aligned sequence output.

	Added clustalo specific input and output types with defintions to
	knowntypes.standard in EMBOSS, and used their names in the ACD
	files.

	Option -cluster for clustering method selection. Removed -mbed
	option.

2010-06-17 Release 0.0.1 (Dubliniensis)

	First "release" as program has been able for a while to perform
	all basic tasks without problems.

	on-standard features already built-in include: HMM-iteration
	(using HMMER for building an HMM) and guide-tree iteration. On top
	of that HMM input works fine and background-frequencies are added
	to the HHalign process.

	Known issues: RNA/DNA alignment is considered buggy. Aligned
	sequences have to be dealigned for HHalign to work properly.

	The HMMER version message can be ignored if no HMM-iteration
	was used.
