###################################################################################
#
# 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 .
#
# The author can be contacted by e-mailing to
# (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 .
#
# The author can be contacted by e-mailing to
# (replace " dot " and " at " with "." and "@", respectively).
#
###################################################################################
#
#
<< README file for the "../Documents/" directory. >>
Currently, it contains four sub-directories: "Blueprints/," "Preprints/," "Presentations/," and "Published/."
* The "Blueprints/" sub-directory stores blueprints (mostly drafts) of ANEX (Ezawa 2020b) and LASTPIECE (Ezawa 2020a).
In a sense, these blueprints are the information sources of the papers (Ezawa 2020a,b,c), which describe the functions and principles of the packages provided in this group.
[NOTE] Because some of the information in these blueprints have NOT been updated properly,
some ideas may be incorrect and/or conflict with those described in the papers (Ezawa 2020a,b,c).
(If you find conflicts, the ideas in the papers are more likely to be correct, or better.)
In any case, when dealing with these blueprints, PLEASE EXCERCISE higher CAUTION than you do when dealing with the papers (preprints).
We will NOT guarantee or warrant ANYTHING.
Every decision and/or action based on these blueprints MUST be done with the self-responsibilities of the readers (or users) themselves.
Nevertheless, the blueprints contain some ideas that are not described in the papers.
The users may want to try (or test) these ideas.
* The "Preprints/" sub-directory stores the preprints of studies on the developments of the packages, "ANEX(_P)" (Ezawa 2020b) and "LASTPIECE(_P)" (Ezawa 2020a), as well as their supplementary functions (Ezawa 2020c).
Currently, three preprints are available:
+ "KEZW_BI_ME00005.lastpiece.pdf," which records the (unpublished) article (Ezawa 2020a);
+ "KEZW_BI_ME00006.anex.pdf," which records the (unpublished) article (Ezawa 2020b);
+ "KEZW_BI_ME00007.srdmap.pdf," which records the (unpublished) article (Ezawa 2020c).
* The "Presentations/" sub-directory stores material files of the past presentations on the ANEX project.
These presentation materials may facilitate the understanding of the backgrounds and motivations, as well as (maybe somewhat outdated) plans, for the project.
Currently, two files are provided:
+ "Ezawa2014.YLseminar20140618_CC4.pdf," which was used for a laboratory seminor in 2014, when I was working under Dr. Tetsushi Yada at Kyushu Institute of Technology.
(Written in Japanese; key words are accompanied with English counterparts.)
+ "ConBio2017_4AT27-01_by_Ezawa&Yada_note_CC4.pdf," which was intended for a preesntation at the ConBio 2017 meeting (held in Kobe, Japan).
(Unfortunately, the presentation was cancelled due to my illness.)
(Written in English, annotated in Japanese; notes below the slides are written in Japanese.)
* The "Published/" sub-directory stores PDF files of articles on the preliminary studies of this project that have been published in peer-reviewed journals, and their additional files other than software packages.
See "readme.Published.txt" in the sub-directory for more details.
< OPEN SOURCE: >
Currently, all files under this directory (i.e., "../Documents/") 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.
--------------------------------------------------------------------------------------------------
[ References ]
* Ezawa K. 2020a. "New perturbation method to compute probabilities of mutually adjoining insertion-type and deletion-type gaps in ancestor-descendant pairwise sequence alignment under genuine sequence evolution model with realistic insertions/deletions: the 'last piece of the puzzle'." (preprint "KEZW_BI_ME00005.lastpiece.pdf" available at: https://www.bioinformatics.org/ftp/pub/anex/Documents/Preprints/; DOI: 10.13140/RG.2.2.32900.14728).
* Ezawa K. 2020b. "Alingment Neighborhood EXplorer (ANEX): First attempt to apply genuine sequence evolution model with realistic insertions/deletions to Multiple Sequence Alignment reconstruction problem." (preprint "KEZW_BI_ME00006.anex.pdf" available at: https://www.bioinformatics.org/ftp/pub/anex/Documents/Preprints/; DOI: 10.13140/RG.2.2.25769.83042).
* Ezawa K. 2020c. "Substitutional Residue-Difference Map (SRD Map) to help locate mis-alignments in Multiple Sequence Alignment (MSA): toward Artificial-Intelilgence-assisted probability distribution of alternative MSAs." (preprint "KEZW_BI_ME00007.srdmap.pdf" available at: https://www.bioinformatics.org/ftp/pub/anex/Documents/Preprints/; DOI: 10.13140/RG.2.2.18220.08320).