###################################################################################
#	
#	ANEX_P (Alignment Neighborhood Explorer, type P):
#	    A package including a program to construct approximate probability distributions of alternative Multiple SEquence Alignments (MSAs)
#	    by exploring the neighborhoods of an input MSA;
#	    the MSA probabilities are computed under a given genuine sequence evolution model with realisric insertions/deletions.
#	   (Written almost exclusively in Perl.)
#
#	Version 0.7: Copyright (C) 2020 Kiyoshi Ezawa
#
#    This package is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This package is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License, "GNU_GPL.txt",
#    along with this package.  If not, see <http://www.gnu.org/licenses/>.
#
#    The author can be contacted by e-mailing to <kezawa dot ezawa3 at gmail dot com>
#    (replace " dot " and " at " with "." and "@", respectively).
#
###################################################################################
#
#
###################################################################################
#	
#	LASTPIECE_P (Local Alignment-STate Probabilities that Insertion-type and dEletion-type gaps Co-Exist, type P):
#	    A package of programs to compute the probabilities of gapped segments in each of which an insertion-type gap and a deletion-type gap co-exist, (which were referred to as case-(iv) gapped segments by (Ezawa 2016a)),
#	    under a stochastic model of sequence evolution with biologically realistic insertions/deletions.
#	   (Written almost exclusively in Perl.)
#
#	Version 0.3: Copyright (C) 2020 Kiyoshi Ezawa
#
#    This package is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This package is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License, "GNU_GPL.txt",
#    along with this package.  If not, see <http://www.gnu.org/licenses/>.
#
#    The author can be contacted by e-mailing to <kezawa dot ezawa3 at gmail dot com>
#    (replace " dot " and " at " with "." and "@", respectively).
#
###################################################################################
#
#

<< README file for the "../Published/" directory. >>

Currently, it contains PDFs of the articles that I (KE) published in 2016,
as well as their supplementary files excluding software packages(, which are available 
elsewhere in the Bioinformatics.org FTP repository (https://www.bioinformatics.org/ftp/pub/)).

Here are the names and brief descriptions of the available files:

* readme.Published.txt
	This file.

* kezawa2016_BMCBioinfo17_133.pdf
	PDF of the main article of (Ezawa 2016a);

* kezawa2016_BMCBioinfo17_133_ADD1.pdf
	PDF of the Additional file 1 of (Ezawa 2016a);

* kezawa2016_BMCBioinfo17_133_ADD3.zip
	ZIP archive of the Additional file 3 of (Ezawa 2016a);

* kezawa2016_BMCBioinfo17_304.pdf
	PDF of the main article of (Ezawa 2016b);

* kezawa2016_BMCBioinfo17_304_ADD1.pdf
	PDF of the Additional file 1 of (Ezawa 2016b);

* kezawa2016_BMCBioinfo17_304_ADD2.pdf
	PDF of the Additional file 2 of (Ezawa 2016b);

* kezawa2016_BMCBioinfo17_397.pdf
	PDF of the main article of (Ezawa 2016c);

* kezawa2016_BMCBioinfo17_397_ADD1.pdf
	PDF of the Additional file 1 of (Ezawa 2016c);

* kezawa2016_BMCBioinfo17_457.pdf
	PDF of the Erratum of (Ezawa 2016b).



< OPEN SOURCE: >
 
Currently,
all files (excpt one, see below) under this directory (i.e., "../Published/") are available under the terms of the 

 Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), 

 which permits unrestricted use, distribution, and reproduction in any medium, 
 PROVIDED THAT you give appropriate credit to
 the original author (K. Ezawa) and the source (the location (URL) of the file(s) you obtained and used),
 provide a link to the Creative Commons license (above), and indicate if changes were made. 

 The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) 
 applies to the data made available in these files, unless otherwise stated.

One exception is the file, "kezawa2016_BMCBioinfo17_133_ADD3.zip,"
to the whole of which the Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies.



--------------------------------------------------------------------------------------------------

[ References ]

  * Ezawa K. 2016a. "Characterizing multiple sequence alignment errors using complete-likelihood score and position-shift map." BMC Bioinformatics 17:133; DOI: 10.1186/s12859-016-0945-5.

  * Ezawa K. 2016b. "General continuous-time Markov model of sequence evolution via insertions/deletions: Are alignment probabilities factorable?" BMC Bioinformatics 17:304; DOI: 10.1186/s12859-016-1105-7; Erratum is also published (BMC Bioinformatics 17:457 ; DOI: 10.1186/s12859-016-1282-4). 

  * Ezawa K. 2016c. "General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation." BMC Bioinformatics 17:397; DOI: 10.1186/s12859-016-1167-6.