ANEX: Alignment Neighborhood EXplorer.

This directory provides two program packages,

	 ANEX (Alignment Neighborhood Explorer)
	and
	LASTPIECE (Local Alignment STate Probabilities that Insertion-type and dEletion-type gaps Co-Exist),

as well as some example outputs and documentations.


<< Table of Contents >> -- as of August 12 (Wed), 2020 --

< Packages >

ANEX_P.ver0.7.tgz
	A gzipped tar archive of the package, ANEX_P (version  0.7),
	which constructs approximate probability distributions of alternative multiple sequence alignments (MSAs)
	by exploring the neighborhoods of a given input (reconstructed) MSA.
	The MSA probabilities are computed under a given genuine sequence evolution model with realistic insertions/deletions (indels).
	The package consists nearly exclusively of Perl scripts and modules, with some Shell scripts for batch analyses or for test purposes.

ANEX_P.ver0.7.1.tgz
	A gzipped tar archive of the LATEST VERSION (ver. 0.7.1)) of ANEX_P.
	

LASTPIECE_P.ver0.3.tgz
	A gzipped tar archive of the package, LASTPIECE_P (version 0.3),
	which quite accurately calculates the probabilities of gap-configurations of gapped segments in ancestor-descendant pairwise alignments (PWAs)
	under a given genuine sequence evolution model with realistic indels.
	The package consists exclusively of Perl scripts and modules.

LASTPIECE_P.ver0.3.1.tgz
	A gzipped tar archive of the LATEST VERSION (ver. 0.3.1) of LASTPIECE_P.


< Example Outputs >

ExOutputs_ANEX.ver0.7.1.tgz
	A gzipped tar-archive of example files output by some scripts of ANEX_P (version 0.7.1).
	See "readme.ExOutputs_ANEX.ver0.7.1.txt" below for more details.

ExOutputs_LASTPIECE.ver0.3.1.tgz
	A gzipped tar-archive of example files output by some scripts of LASTPIECE_P (version 0.3.1).
	See "readme.ExOutputs_LASTPIECE.ver0.3.1.txt" below for more details.


< Documentations >

Documents/
	Directory storing some documentation files.
	Currently, there are four sub-directories, "Blueprints/," "Preprints/," "Presentations/" and "Published/."
	See the readme.Documents.txt file for more details.



< README files >

readme.ANEX_P.ver0.7.1.txt
	Description of the package, ANEX_P (version  0.7.1).
	(It is identical to the "README.txt" file at the top directory extracted from "ANEX_P.ver0.7.1.tgz.")

readme.Documents.txt
	Description of the documentation files, including preprints and blueprints,
	that are stored under the directory, "Documents/."
	(It is identical to the file of the same name in the directory, "Documents/.")

readme.ExOutputs_ANEX.ver0.7.1.txt
	Description of the archive, "ExOutputs_ANEX.ver0.7.1.tgz."
	(It is identical to the "README.ExOutputs_ANEX.ver0.7.txt" file at the top directory extracted from the archive.)

readme.ExOutputs_LASTPIECE.ver0.3.1.txt
	Description of the archive, "ExOutputs_LASTPIECE.ver0.3.1.tgz."
	(It is identical to the "README.ExOutputs_LASTPIECE.ver0.3.txt" file at the top directory extracted from the archive.)

readme.LASTPIECE_P.ver0.3.1.txt
	Description of the package, LASTPIECE_P (version 0.3.1).
	(It is identical to the "README.txt" file at the top directory extracted from "LASTPIECE_P.ver0.3.1.tgz.")