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authorNorbert Preining <norbert@preining.info>2019-09-02 13:46:59 +0900
committerNorbert Preining <norbert@preining.info>2019-09-02 13:46:59 +0900
commite0c6872cf40896c7be36b11dcc744620f10adf1d (patch)
tree60335e10d2f4354b0674ec22d7b53f0f8abee672 /macros/latex/contrib/gotoh
Initial commit
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-rw-r--r--macros/latex/contrib/gotoh/LICENSE21
-rw-r--r--macros/latex/contrib/gotoh/README.md35
-rw-r--r--macros/latex/contrib/gotoh/gotoh.dtx931
-rw-r--r--macros/latex/contrib/gotoh/gotoh.ins26
-rw-r--r--macros/latex/contrib/gotoh/gotoh.pdfbin0 -> 291216 bytes
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diff --git a/macros/latex/contrib/gotoh/LICENSE b/macros/latex/contrib/gotoh/LICENSE
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@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 Watson (wtsnjp)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/macros/latex/contrib/gotoh/README.md b/macros/latex/contrib/gotoh/README.md
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+# Package Gotoh (v1.1)
+
+
+LaTeX package: An implementation of the Gotoh sequence alignment algorithm.
+
+## System Requirements
+
+* TeX format: LaTeX2e
+* TeX engine: any engine
+* Document class: any class
+* Prerequisite package: xkeyval
+
+## Installation
+
+To install the package, interpret the `gotoh.ins` file with LaTeX.
+
+```
+latex gotoh.ins
+```
+
+Then move the files as follows (in a system compliant to TDS 1.1).
+
+* `*.sty`: $TEXMF/tex/latex/gotoh/
+* `*.dtx`, `*.ins`: $TEXMF/source/latex/gotoh/
+* `*.pdf`, `*.tex`: $TEXMF/doc/latex/gotoh/
+
+And rehash your TEXMF trees if necessary.
+
+## License
+
+This package is distributed under [the MIT license](./LICENSE).
+
+---
+
+Takuto ASAKURA ([wtsnjp](https://twitter.com/wtsnjp))
diff --git a/macros/latex/contrib/gotoh/gotoh.dtx b/macros/latex/contrib/gotoh/gotoh.dtx
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+% ^^A -*- latex -*-
+% \iffalse meta-comment
+%
+% This is file `gotoh.dtx'.
+%
+% Copyright (c) 2017 Takuto ASAKURA (wtsnjp)
+% GitHub: https://github.com/wtsnjp
+% Twitter: @wtsnjp
+%
+% This package is distributed under the MIT License.
+%
+% \fi
+%
+% \CheckSum{984}
+%
+% \changes{v1.0}{2017/05/05}{The first version}
+%
+% \iffalse
+%<*package>
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{gotoh}[2017/07/07 v1.1 Sequence alignment algorithm]
+%</package>
+%<*driver>
+\documentclass[draft]{ltxdoc}
+\usepackage{amsmath}
+\usepackage{enumitem}
+\usepackage{gotoh}
+\EnableCrossrefs
+\CodelineIndex
+\RecordChanges
+\setlength\hfuzz{15pt}
+\hbadness=7000
+\newcommand{\pkgName}[1]{\textsf{#1}}
+\newcommand{\pkgGotoh}{\pkgName{Gotoh}}
+\newcommand{\synKey}[1]{\texttt{#1}}
+\newcommand{\synOr}{\quad or\quad}
+\newcommand{\synBool}{\meta{\normalfont\texttt{true\textbar false}}}
+\newcommand{\defeq}{\equiv}
+\newcommand{\eqsep}{\;}
+\setlist[description]{font={\normalfont}}
+\begin{document}
+\DocInput{gotoh.dtx}
+\end{document}
+%</driver>
+% \fi
+%
+% \CharacterTable
+% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
+% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
+% Digits \0\1\2\3\4\5\6\7\8\9
+% Exclamation \! Double quote \" Hash (number) \#
+% Dollar \$ Percent \% Ampersand \&
+% Acute accent \' Left paren \( Right paren \)
+% Asterisk \* Plus \+ Comma \,
+% Minus \- Point \. Solidus \/
+% Colon \: Semicolon \; Less than \<
+% Equals \= Greater than \> Question mark \?
+% Commercial at \@ Left bracket \[ Backslash \\
+% Right bracket \] Circumflex \^ Underscore \_
+% Grave accent \` Left brace \{ Vertical bar \|
+% Right brace \} Tilde \~}
+%
+% \GetFileInfo{gotoh.sty}
+%
+% \DoNotIndex{%
+% \@empty,\@ne,\\,\advance,\bgroup,\csname,\def,\do,\edef,\egroup,\else,%
+% \endcsname,\expandafter,\fi,\global,\hbox,\hss,\ht,\let,\m@ne,\mbox,%
+% \multiply,\newcommand,\newcount,\newdimen,\newif,\number,\PackageError,%
+% \PackageWarningNoLine,\relax,\RequirePackage,\sbox,\texttt,\the,\xdef,\z@}
+%
+% \title{The {\pkgGotoh} package}
+% \author{Takuto ASAKURA (wtsnjp)}
+% \date{{\fileversion} [\filedate]}
+% \maketitle
+%
+% \MakeShortVerb{\|}
+%
+% \begin{abstract}
+% This package is an implementation in {\TeX} of the Gotoh algorithm, which
+% calculates biological sequence alignments. The package provides only two user
+% commands: |\Gotoh| for executing the algorithm and |\GotohConfig| for setting
+% various parameters with a key-value list.
+% \end{abstract}
+%
+% ^^A\tableofcontents
+%
+% \section{System Requirements}
+%
+% System requirements of {\pkgGotoh} are shown bellow.
+% \begin{itemize}
+% \item {\TeX} engine: any engine
+% \item {\TeX} format: {\LaTeXe}
+% \item Document class: any class
+% \item Required package: \pkgName{xkeyval}
+% \end{itemize}
+%
+% \section{Loading the {\pkgGotoh} Package}
+%
+% To use the {\pkgGotoh} package, load |gotoh.sty| with |\usepackage| command
+% in preamble. No package option is available.
+% \begin{quote}
+% |\usepackage{gotoh}|
+% \end{quote}
+%
+% \section{Calculating the Alignment}
+%
+% \DescribeMacro{\Gotoh}
+% The syntax of |\Gotoh| is shown below.
+% \begin{quote}
+% |\Gotoh|\oarg{key-value list}\marg{sequence A}\marg{sequence B}
+% \end{quote}
+% The command puts the optimal score of the alignment to specified control
+% sequence (default: |\GotohScore|) after executing the Gotoh algorithm, and
+% returns the alignment results to other control sequences (default:
+% |\GotohResultA| and |\GotohResultB|). Note that these assignments are done
+% globally. Using the optional argument, you can change the configuration
+% temporary with the same keys in |\GotohConfig| (see the next section).
+%
+% \section{Configuration}
+%
+% \DescribeMacro{\GotohConfig}
+% You can change various settings and parameters related to this package with
+% |\GotohConfig| command. The command takes a key-value list of the settings as
+% its argument and changes the values locally.
+% \begin{quote}
+% |\GotohConfig|\marg{key-value list}
+% \end{quote}
+%
+% \subsection{Control Sequences to Store Results}
+%
+% \DescribeMacro{\GotohScore}
+% \DescribeMacro{\GotohResultA}
+% \DescribeMacro{\GotohResultB}
+% Control sequences which |\Gotoh| command return results can be specified with
+% following keys:
+%
+% \begin{description}
+% \item[\synKey{score} |=| \meta{control sequence}]\hfill |\GotohScore| \\
+% sets the control sequence to store optimal score of the last alignment
+% which calculated by |\Gotoh| command.
+% \item[\synKey{result A} |=| \meta{control sequence}]\hfill |\GotohResultA|
+% \item[\synKey{result B} |=| \meta{control sequence}]\hfill |\GotohResultB| \\
+% specify the control sequences to store alignment results respectively
+% corresponding to \meta{sequence A} and \meta{sequence B} of the arguments
+% of |\Gotoh|.
+% \end{description}
+%
+% \subsection{Algorithm Parameters}
+%
+% The default value of algorithm parameters which define the scoring are
+% \begin{equation}
+% \mathrm{match} = 1,\eqsep \mathrm{mismatch} = -1,\eqsep d = 7,\eqsep e= 1.
+% \label{eq:parameters}
+% \end{equation}
+% Parameters $\mathrm{match}, \mathrm{mismatch}$ define the penalties of a
+% \emph{match} and \emph{mismatch} respectively, and $d, e$ are used in a gap
+% penalty (see section \ref{sect:calc}). The parameters appeared in the above
+% equations are able to be changed with following keys:
+%
+% \begin{description}
+% \item[\synKey{match} |=| \meta{number}]\hfill |1|
+% \item[\synKey{mismatch} |=| \meta{number}]\hfill |-1|
+% \item[\synKey{d} |=| \meta{number}]\hfill |7|
+% \item[\synKey{e} |=| \meta{number}]\hfill |1| \\
+% set the parameters appear in the above equations.
+% \end{description}
+%
+% Though the |\Gotoh| command calculates sequence alignment with standard
+% dynamic programming as default, you can use memoization functions instead.
+% Note that both of the methods produce exactly the same results.
+%
+% \begin{description}
+% \item[\synKey{memoization} |=| \synBool \synOr \synKey{memoization}]\hfill |false| \\
+% If true, use memoization functions to execute the Gotoh algorithm.
+% \end{description}
+%
+% \subsection{Others}
+%
+% \begin{description}
+% \item[\synKey{gap char} |=| \meta{character}]\hfill |.| (period) \\
+% is inserted to the alignment results where gaps appear. Note that you have
+% to be careful if using |-| (hyphen) as gap characters because successive
+% hyphens automatically converted to dashes by {\TeX}. In this case, you can
+% specify |\mbox{-}| instead.
+% \item[\synKey{uppercase} |=| \synBool \synOr \synKey{uppercase}]\hfill |false| \\
+% If true, uppercase both \meta{sequence A} and \meta{sequence B} before
+% executing the algorithm.
+% \end{description}
+%
+% \StopEventually{\PrintIndex\PrintChanges}
+%
+% \section{Algorithm and Implementation}
+%
+% \subsection{Required package}
+%
+% Package \pkgName{xkeyval} is required to process key-value lists.
+% \begin{macrocode}
+\RequirePackage{xkeyval}
+% \end{macrocode}
+%
+% \subsection{Messages}
+%
+% \begin{macro}{\gth@warn}
+% \begin{macro}{\gth@error}
+% Commands for warning and error messages.
+% \begin{macrocode}
+\def\gth@pkgname{gotoh}
+\def\gth@warn{\PackageWarningNoLine\gth@pkgname}
+\def\gth@error{\PackageError\gth@pkgname}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+%
+% \subsection{Switches, Registers and Constants}
+%
+% All boolean switches, count registers and dimen registers used by this
+% package are declared here.
+%
+% \begin{macro}{\if@gth@first@}
+% \begin{macro}{\if@gth@renain@}
+% \begin{macro}{\if@gth@gap@}
+% \begin{macro}{\if@gth@gapx@}
+% \begin{macro}{\if@gth@gapy@}
+% A switch |\if@gth@first@| is for a calculation command |\gth@max|, and the
+% other switches are for trace back (in macro |\gth@gotoh|).
+% \begin{macrocode}
+\newif\if@gth@first@
+\newif\if@gth@remain@
+\newif\if@gth@gap@
+\newif\if@gth@gapx@
+\newif\if@gth@gapy@
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \begin{macro}{\gth@tempcnta}
+% \begin{macro}{\gth@tempcntb}
+% \begin{macro}{\gth@tempcntc}
+% \begin{macro}{\gth@tempcntd}
+% \begin{macro}{\gth@calc}
+% Scratch four count registers for general use and one for some calculation
+% routines.
+% \begin{macrocode}
+\newcount\gth@tempcnta
+\newcount\gth@tempcntb
+\newcount\gth@tempcntc
+\newcount\gth@tempcntd
+\newcount\gth@calc
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \begin{macro}{\gth@sn}
+% This is \emph{not} a counter register but a macro to store \meta{number}
+% which is used as `serial number'.
+% \begin{macrocode}
+\edef\gth@sn{\number\z@}
+% \end{macrocode}
+% \end{macro}
+%
+% \begin{macro}{\gth@min}
+% This macro stores a large negative \meta{number} which is used instead of
+% $-\infty$. Here |\gth@M| is a largest constant which can be defined by
+% |\mathchardef| primitive (in traditional {\TeX} engine).
+% \begin{macrocode}
+\mathchardef\gth@M="7FFF
+\edef\gth@min{-\number\gth@M}
+% \end{macrocode}
+% \end{macro}
+%
+% \begin{macro}{\gth@tempdima}
+% Scratch a dimen register for general use.
+% \begin{macrocode}
+\newdimen\gth@tempdima
+% \end{macrocode}
+% \end{macro}
+%
+% \subsection{Defining and Setting Keys}
+%
+% \begin{macro}{\gth@match}
+% \begin{macro}{\gth@mismatch}
+% \begin{macro}{\gth@d}
+% \begin{macro}{\gth@e}
+% These are keys for setting the parameters of the algorithm. The default
+% values which are shown in Equations~(\ref{eq:parameters}) are set here, and
+% stored in the macros (\emph{not} count registers) respectively.
+% \begin{macrocode}
+\define@cmdkeys[gth]{config}[gth@]{match, mismatch, d, e}
+\setkeys[gth]{config}{match=1, mismatch=-1, d=7, e=1}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \begin{macro}{\gth@score}
+% \begin{macro}{\gth@resulta}
+% \begin{macro}{\gth@resultb}
+% The macros to store the result of the algorithms are also stored in internal
+% macros.
+% \begin{macrocode}
+\define@key[gth]{config}{score}{\def\gth@score{#1}}
+\define@key[gth]{config}{result A}{\def\gth@resulta{#1}}
+\define@key[gth]{config}{result B}{\def\gth@resultb{#1}}
+\setkeys[gth]{config}{
+ score=\GotohScore, result A=\GotohResultA, result B=\GotohResultB}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \begin{macro}{\if@gth@memoization}
+% \begin{macro}{\if@gth@uppercase}
+% \begin{macro}{\gth@gap@char}
+% Both boolean keys |\if@gth@memoization| and |\if@gth@uppercase| are set false
+% as default. The gap char is stored in |\gth@gap@char|.
+% \begin{macrocode}
+\define@boolkeys[gth]{config}[@gth@]{memoization, uppercase}[true]
+\define@key[gth]{config}{gap char}{\def\gth@gap@char{#1}}
+\setkeys[gth]{config}{memoization=false, uppercase=false, gap char={.}}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \subsection{Utility Commands}
+%
+% \begin{macro}{\gth@nameuse}
+% \begin{macro}{\gth@name@edef}
+% \begin{macro}{\gth@name@xdef}
+% \begin{macro}{\gth@glet}
+% Some primitives to use, define or copy control sequences are wrapped.
+% \begin{macrocode}
+\def\gth@nameuse#1{\csname gth@#1\endcsname}
+\def\gth@name@edef#1{\expandafter\edef\csname gth@#1\endcsname}
+\def\gth@name@xdef#1{\expandafter\xdef\csname gth@#1\endcsname}
+\def\gth@glet{\global\let}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \begin{macro}{\gth@advance}
+% \begin{macro}{\gth@increment}
+% \begin{macro}{\gth@decrement}
+% Commands to treate macros which store \meta{number} like count registers.
+% \begin{macrocode}
+\def\gth@advance#1#2{%
+ \gth@calc#1\advance\gth@calc#2\edef#1{\the\gth@calc}}
+\def\gth@increment#1{\gth@advance#1\@ne}
+\def\gth@decrement#1{\gth@advance#1\m@ne}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \subsection{Calculation Routines}\label{sect:calc}
+%
+% Since these calculation routines (macros) are \emph{not} full expandable, all
+% commands defined here return the results by storing the value in the counter
+% register |\gth@calc|. This assignments are done locally.
+%
+% \begin{macro}{\gth@max}
+% This command take comma-separated list of \meta{number} and returns the max
+% value of them.
+% \begin{macrocode}
+\def\gth@max#1{%
+ \@gth@first@true
+ \@for\gth@member:=#1\do{%
+ \if@gth@first@
+ \gth@calc\gth@member
+ \@gth@first@false
+ \else
+ \ifnum\gth@member>\gth@calc
+ \gth@calc\gth@member
+ \fi
+ \fi}}
+% \end{macrocode}
+% \end{macro}
+%
+% \begin{macro}{\gth@gap@penalty}
+% This command takes $l$, the length of a \emph{gap}, as its argument and
+% calculates its penalty which defined by following function\footnote{This form
+% of gap penalty is called `Affine gaps'.}:
+% \begin{equation}
+% g(l) = -d - (l-1)e. \label{eq:gap}
+% \end{equation}
+% In this equation, $d$ and $e$ are parameters of the algorithm, which have
+% default values shown in Equations~(\ref{eq:parameters}).
+% \begin{macrocode}
+\def\gth@gap@penalty#1{%
+ \gth@calc#1\relax
+ \advance\gth@calc\m@ne
+ \multiply\gth@calc-\gth@e
+ \advance\gth@calc-\gth@d}
+% \end{macrocode}
+% \end{macro}
+%
+% \subsection{Printing Matrices}
+%
+% \begin{macro}{\gth@print@matrix}
+% This command shows the matrices $M$, $I^x$ or $I^y$ (See
+% section~\ref{sect:algorithm}). The argument of this macro specifies which
+% matrix to show, so you can detect |m|, |ix|, or |iy|. However, this macro is
+% currently only for the author of this package to debug.
+% \begin{macrocode}
+\def\gth@tab#1{%
+ \bgroup
+ \sbox\z@ 0%
+ \expandafter\gth@tempdima\ht\z@
+ \multiply\gth@tempdima 8%
+ \mbox{\hbox to\gth@tempdima{\hss #1}}%
+ \egroup}
+\def\gth@print@matrix#1{%
+ \bgroup\ttfamily
+ #1:\\
+ \gth@tempcnta\z@
+ \@whilenum\gth@tempcnta<\gth@m\do{%
+ \gth@tempcntb\z@
+ \@whilenum\gth@tempcntb<\gth@n\do{%
+ \gth@tab{%
+ \gth@nameuse{\gth@sn @#1@\the\gth@tempcnta
+ @\the\gth@tempcntb}}%
+ \advance\gth@tempcntb\@ne}\\
+ \advance\gth@tempcnta\@ne}%
+ \egroup}
+% \end{macrocode}
+% \end{macro}
+%
+% \subsection{Executing the Gotoh Algorithm}\label{sect:algorithm}
+%
+% \begin{macro}{\Gotoh}
+% \changes{v1.1}{2017/07/07}{Add a new optional argument for changing
+% config temporary}
+% This is the user interface to execute the Gotoh algorithm. First, the
+% `serial number' is incremented. The whole other process executed by this
+% macro contained in a group because a number of temporary macros are defined
+% during processing.
+% \begin{macrocode}
+\newcommand{\Gotoh}{%
+ \gth@increment\gth@sn
+ \bgroup % \egroup is in \gth@gotoh@pre
+ \@ifnextchar[{\gth@gotoh@setkeys}{\gth@gotoh@pre}}
+% \end{macrocode}
+% \end{macro}
+%
+% \begin{macro}{\gth@gotoh@setkeys}
+% \begin{macro}{\gth@gotoh@pre}
+% These inner macros are for preparing: |\gth@gotoh@setkeys| process temporary
+% configuration specified with the optional argument of |\Gotoh|. In
+% |\gth@gotoh@pre|, if the boolean switch |\if@gth@uppercase| is true, the
+% arguments are processed by |\uppercase| preamble before passing them to
+% |\gth@gotoh| macro.
+% \begin{macrocode}
+\def\gth@gotoh@setkeys[#1]{\setkeys[gth]{config}{#1}\gth@gotoh@pre}
+\def\gth@gotoh@pre#1#2{%
+ \edef\gth@tmpa{\noexpand\gth@gotoh{#1}{#2}}%
+ \if@gth@uppercase
+ \uppercase\expandafter{\gth@tmpa}%
+ \else
+ \gth@tmpa
+ \fi\egroup}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+%
+% \begin{macro}{\gth@gotoh}
+% This macro actually executes the Gotoh algorithm~\cite{gotoh1982}. The input
+% of the algorithm is two biological sequences
+% \[
+% A \defeq a_1a_2a_3\dots a_m,\eqsep B \defeq b_1b_2b_3\dots b_n
+% \]
+% where $a_i$ and $b_j$ are chosen from a finite alphabet, e.g.~$\{\mathrm{A},
+% \mathrm{T}, \mathrm{G}, \mathrm{C}\}$. The command takes these sequences as
+% its arguments, and calculate following recurrence formula\footnote{This
+% calculation is done in $O(mn)$ time.} to get optimal score of the algorithm:
+% \begin{equation}
+% M_{i+1, j+1}
+% = \max\left\{M_{ij}, I^x_{ij}, I^y_{ij}\right\} + c_{ij}
+% \label{eq:m}
+% \end{equation}
+% where
+% \begin{align}
+% I^x_{i+1, j} &= \max\left\{ M_{ij}-d, I^x_{ij}-e, I^y_{ij}-d \right\},
+% \label{eq:ix} \\
+% I^y_{i, j+1} &= \max\left\{ M_{ij}-d, I^y_{ij}-e \right\},
+% \label{eq:iy}
+% \end{align}
+% and $c_{ij}$ is a score for a pair $(a_i, b_j)$, namely
+% \[
+% c_{ij} = \left\{
+% \begin{array}{rll}
+% 1 & \text{if\enspace} a_i = b_j & \text{(match)} \\
+% -1 & \text{otherwise} & \text{(mismatch)}. \\
+% \end{array}
+% \right.
+% \]
+% Note that the Equations (\ref{eq:ix}) and (\ref{eq:iy}) have asymmetric form
+% because the order of inserting \emph{gaps} when alternating $A$ and $B$ does
+% not affect the optimal score.
+%
+% \subsubsection{Getting sequences}
+%
+% \begin{macro}{\gth@m}
+% \begin{macro}{\gth@n}
+% Here each calacters $a_i, b_j$ in the input sequences are stored in
+% |\gth@seqa@|$a_i$ and |\gth@seqa@|$b_j$, and the lengthes of the sequences
+% $m, n$ are stored in |\gth@m| and |\gth@n| respectively.
+% \begin{macrocode}
+\def\gth@gotoh#1#2{%
+ \gth@tempcnta\z@
+ \@tfor\gth@member:=#1\do{%
+ \gth@name@edef{seqa@\the\gth@tempcnta}{\gth@member}%
+ \advance\gth@tempcnta\@ne}%
+ \advance\gth@tempcnta\@ne
+ \edef\gth@m{\the\gth@tempcnta}%
+ \gth@tempcntb\z@
+ \@tfor\gth@member:=#2\do{%
+ \gth@name@edef{seqb@\the\gth@tempcntb}{\gth@member}%
+ \advance\gth@tempcntb\@ne}%
+ \advance\gth@tempcntb\@ne
+ \edef\gth@n{\the\gth@tempcntb}%
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+%
+% \subsubsection{Initialization}
+%
+% We have to be careful with initialization because many implementations of the
+% Gotoh algorithm have problems here~\cite{flouri2015}. Specifically, the
+% package initialzes the matrxes with following equations:
+% \begin{align*}
+% M_{i0} &= -\infty, M_{0j} = -\infty, M_{00} = 0, \\
+% I^x_{i0} &= -g(i), I^x_{0j} = -\infty, \\
+% I^y_{i0} &= -\infty, I^y_{0j} = -g(j).
+% \end{align*}
+% Note that function $g(l)$ is a gap penalty (shown in Equation~(\ref{eq:gap}))
+% and can be calculated with the macro |\gth@gap@penalty|.
+%
+% \begin{macrocode}
+ \gth@tempcnta\z@
+ \@whilenum\gth@tempcnta<\gth@m\do{%
+ \gth@gap@penalty{\gth@tempcnta}%
+ \gth@name@xdef{\gth@sn @m@\the\gth@tempcnta @0}{\gth@min}%
+ \gth@name@xdef{\gth@sn @ix@\the\gth@tempcnta @0}{\the\gth@calc}%
+ \gth@name@xdef{\gth@sn @iy@\the\gth@tempcnta @0}{\gth@min}%
+ \advance\gth@tempcnta\@ne}%
+ \gth@tempcntb\z@
+ \@whilenum\gth@tempcntb<\gth@n\do{%
+ \gth@gap@penalty{\gth@tempcntb}%
+ \gth@name@xdef{\gth@sn @m@0@\the\gth@tempcntb}{\gth@min}%
+ \gth@name@xdef{\gth@sn @ix@0@\the\gth@tempcntb}{\gth@min}%
+ \gth@name@xdef{\gth@sn @iy@0@\the\gth@tempcntb}{\the\gth@calc}%
+ \advance\gth@tempcntb\@ne}%
+ \gth@name@xdef{\gth@sn @m@0@0}{\number\z@}%
+% \end{macrocode}
+%
+% \subsubsection{Memoization}
+%
+% If the switch |\if@gth@memoization| is true, memoization functions (See
+% section~\ref{sect:memofunc}) are called recursively.
+% \begin{macrocode}
+ \if@gth@memoization
+ \gth@decrement\gth@m \gth@decrement\gth@n
+ \gth@memo@ix{\gth@m}{\gth@n}%
+ \gth@memo@iy{\gth@m}{\gth@n}%
+ \gth@memo@m{\gth@m}{\gth@n}%
+ \gth@increment\gth@m \gth@increment\gth@n
+% \end{macrocode}
+%
+% \subsubsection{Dynamic Programming}
+%
+% To fill matrxes $M$, $I^x$, and $I^y$ the package use the recurrence formula
+%
+% \begin{macrocode}
+ \else
+ \gth@tempcnta\@ne
+ \@whilenum\gth@tempcnta<\gth@m\do{%
+ \gth@tempcntb\@ne
+ \@whilenum\gth@tempcntb<\gth@n\do{%
+% \end{macrocode}
+% First, $I^x$ is calculated with Equation (\ref{eq:ix}).
+% \begin{macrocode}
+ \advance\gth@tempcnta\m@ne
+ \gth@max{%
+ \gth@nameuse{\gth@sn @m@\the\gth@tempcnta
+ @\the\gth@tempcntb},%
+ \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta
+ @\the\gth@tempcntb}}%
+ \gth@tempcntc\gth@calc
+ \gth@tempcntd
+ \gth@nameuse{\gth@sn @ix@\the\gth@tempcnta
+ @\the\gth@tempcntb}%
+ \advance\gth@tempcntc-\gth@d\advance\gth@tempcntd-\gth@e
+ \advance\gth@tempcnta\@ne
+ \gth@max{\gth@tempcntc,\gth@tempcntd}%
+ \gth@name@xdef{\gth@sn @ix@\the\gth@tempcnta
+ @\the\gth@tempcntb}{%
+ \the\gth@calc}%
+% \end{macrocode}
+% Secondly, $I^y$ is calculated with Equation (\ref{eq:iy}).
+% \begin{macrocode}
+ \advance\gth@tempcntb\m@ne
+ \gth@tempcntc
+ \gth@nameuse{\gth@sn @m@\the\gth@tempcnta
+ @\the\gth@tempcntb}%
+ \gth@tempcntd
+ \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta
+ @\the\gth@tempcntb}%
+ \advance\gth@tempcntc-\gth@d\advance\gth@tempcntd-\gth@e
+ \advance\gth@tempcntb\@ne
+ \gth@max{\gth@tempcntc,\gth@tempcntd}%
+ \gth@name@xdef{\gth@sn @iy@\the\gth@tempcnta
+ @\the\gth@tempcntb}{%
+ \the\gth@calc}%
+% \end{macrocode}
+% Finally, $M$ is calculated with Equation (\ref{eq:m}) and a loop is completed.
+% \begin{macrocode}
+ \advance\gth@tempcnta\m@ne\advance\gth@tempcntb\m@ne
+ \gth@max{%
+ \gth@nameuse{\gth@sn @m@\the\gth@tempcnta
+ @\the\gth@tempcntb},%
+ \gth@nameuse{\gth@sn @ix@\the\gth@tempcnta
+ @\the\gth@tempcntb},%
+ \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta
+ @\the\gth@tempcntb}}%
+ \edef\gth@tmpa{\gth@nameuse{seqa@\the\gth@tempcnta}}%
+ \edef\gth@tmpb{\gth@nameuse{seqb@\the\gth@tempcntb}}%
+ \advance\gth@tempcnta\@ne\advance\gth@tempcntb\@ne
+ \ifx\gth@tmpa\gth@tmpb
+ \advance\gth@calc\gth@match
+ \else
+ \advance\gth@calc\gth@mismatch
+ \fi
+ \gth@name@xdef{\gth@sn @m@\the\gth@tempcnta
+ @\the\gth@tempcntb}{%
+ \the\gth@calc}%
+ \advance\gth@tempcntb\@ne}%
+ \advance\gth@tempcnta\@ne}%
+ \fi
+% \end{macrocode}
+%
+% \subsubsection{Printing Matrices}
+%
+% This is piece of code for debugging the package (so usually commented out).
+%
+% \begin{macrocode}
+ %\gth@print@matrix{m}%
+ %\gth@print@matrix{ix}%
+ %\gth@print@matrix{iy}%
+% \end{macrocode}
+%
+% \subsubsection{Returning the Optimal Score}
+%
+% The calculated optimal score of the alignment stored here to the control
+% sequences which stored in |\gth@score|.
+% \begin{macrocode}
+ \bgroup
+ \gth@decrement\gth@m \gth@decrement\gth@n
+ \expandafter\xdef\gth@score{%
+ \gth@nameuse{\gth@sn @m@\gth@m @\gth@n}}%
+ \egroup
+% \end{macrocode}
+%
+% \subsubsection{Trace Back}
+%
+% After processing dynamic programming (or memoization functions), matrices
+% $M$, $I^x$, and $I^y$ are all filled. Using these matrices, we can determine
+% the `trace' from the optimal score $M_{m,n}$ to the start $M_{0,0}$ and get
+% the result of alignment $(x, y)$.
+%
+% Considering the form of Equation (\ref{eq:m})--(\ref{eq:iy}), the calculation
+% formulae of the former values depend on which matrix the `current position'
+% exists. In order to take into account these differences, trace back process
+% is calculated while switching three modes: default, gap x, and gap y.
+%
+% First, make sure to empty |\gth@rseq@x| and |\gth@rseq@y| which is going to
+% store result alignment sequences $x$ and $y$ respectively. Note that this is
+% the trace \emph{back} process, so new characters are prepended to the
+% existing sequences in each loop. In the next line, the switches
+% |\if@gth@gapx@| and |\if@gth@gapy@| are both turned off (which means
+% processing starts from the default mode).
+% \begin{macrocode}
+ \let\gth@rseq@x\@empty\let\gth@rseq@y\@empty
+ \@gth@remain@true\@gth@gapx@false\@gth@gapy@false
+% \end{macrocode}
+% In the main loop of trace back, process the condition either $x$ or $y$ is
+% already completed first. In this situation, the other sequence should be
+% filled all the remaining with \emph{gaps}.
+% \begin{macrocode}
+ \@whilesw\if@gth@remain@\fi{%
+ \ifnum\gth@m=\z@
+ \gth@decrement\gth@n
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{seqb@\gth@n}\relax\else
+ \edef\gth@rseq@x{\gth@gap@char\gth@rseq@x}%
+ \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}%
+ \gth@rseq@y}%
+ \fi
+ \else\ifnum\gth@n=\z@
+ \gth@decrement\gth@m
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{seqa@\gth@m}\relax\else
+ \edef\gth@rseq@x{\gth@nameuse{seqa@\gth@m}%
+ \gth@rseq@x}%
+ \edef\gth@rseq@y{\gth@gap@char\gth@rseq@y}%
+ \fi
+ \else
+% \end{macrocode}
+% \paragraph{mode: gap x}
+% Prepend former base to $x$ and a \emph{gap} to $y$. If
+% $M_{m-1,n}-d>I^x_{m-1,n}-e$ back to default mode. Else if
+% $I^x_{m-1,n}-e<I^y_{m-1,n}-d$ switch to mode gap y and otherwise stay in mode
+% gap x.
+% \begin{macrocode}
+ \if@gth@gapx@
+ \gth@decrement\gth@m
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{seqa@\gth@m}\relax\else
+ \edef\gth@rseq@x{\gth@nameuse{seqa@\gth@m}%
+ \gth@rseq@x}%
+ \edef\gth@rseq@y{\gth@gap@char\gth@rseq@y}%
+ \fi
+ \gth@tempcnta\gth@nameuse{\gth@sn @m@\gth@m @\gth@n}%
+ \gth@tempcntb\gth@nameuse{\gth@sn @ix@\gth@m @\gth@n}%
+ \gth@tempcntc\gth@nameuse{\gth@sn @iy@\gth@m @\gth@n}%
+ \advance\gth@tempcnta-\gth@d
+ \advance\gth@tempcntb-\gth@e
+ \advance\gth@tempcntc-\gth@d
+ \ifnum\gth@tempcnta>\gth@tempcntb
+ \@gth@gapx@false
+ \else\ifnum\gth@tempcntb<\gth@tempcntc
+ \@gth@gapx@false\@gth@gapy@true
+ \fi\fi
+% \end{macrocode}
+% \paragraph{mode: gap y}
+% Prepend a \emph{gap} to $x$ and former base to $y$. If
+% $M_{m,n-1}-d>I^y_{m,n-1}-e$ back to default mode and otherwise stay in mode
+% gap y.
+% \begin{macrocode}
+ \else\if@gth@gapy@
+ \gth@decrement\gth@n
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{seqb@\gth@n}\relax\else
+ \edef\gth@rseq@x{\gth@gap@char\gth@rseq@x}%
+ \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}%
+ \gth@rseq@y}%
+ \fi
+ \gth@tempcnta\gth@nameuse{\gth@sn @m@\gth@m @\gth@n}%
+ \gth@tempcntb\gth@nameuse{\gth@sn @iy@\gth@m @\gth@n}%
+ \advance\gth@tempcnta-\gth@d\advance\gth@tempcntb-\gth@e
+ \ifnum\gth@tempcnta>\gth@tempcntb
+ \@gth@gapy@false
+ \fi
+% \end{macrocode}
+% \paragraph{mode: default}
+% Prepend former base to $x$ and $y$ respectively. Only if
+% $M_{m-1,n-1}>I^x_{m-1,n-1}$ and $M_{m-1,n-1}>I^y_{m-1,n-1}$ stay on default
+% mode, and else if $I^x_{m-1,n-1}>I^y_{n-1,m-1}$ go to gap x otherwise go to
+% gap y.
+% \begin{macrocode}
+ \else
+ \gth@decrement\gth@m
+ \gth@decrement\gth@n
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{seqa@\gth@m}\relax\else
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{seqb@\gth@n}\relax\else
+ \edef\gth@rseq@x{\gth@nameuse{seqa@\gth@m}%
+ \gth@rseq@x}%
+ \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}%
+ \gth@rseq@y}%
+ \fi
+ \fi
+ \gth@tempcnta\gth@nameuse{\gth@sn @m@\gth@m @\gth@n}%
+ \gth@tempcntb\gth@nameuse{\gth@sn @ix@\gth@m @\gth@n}%
+ \gth@tempcntc\gth@nameuse{\gth@sn @iy@\gth@m @\gth@n}%
+ \@gth@gap@false
+ \ifnum\gth@tempcnta<\gth@tempcntb\@gth@gap@true\fi
+ \ifnum\gth@tempcnta<\gth@tempcntc\@gth@gap@true\fi
+ \if@gth@gap@
+ \ifnum\gth@tempcntb>\gth@tempcntc
+ \@gth@gapx@true
+ \else
+ \@gth@gapy@true
+ \fi
+ \fi
+ \fi\fi
+ \fi\fi
+% \end{macrocode}
+% Finally, if we achieve to $M_{0,0}$, exit from the main loop.
+% \begin{macrocode}
+ \ifnum\gth@m<\@ne\ifnum\gth@n<\@ne
+ \@gth@remain@false
+ \fi\fi}%
+% \end{macrocode}
+%
+% \subsubsection{Returning Results}
+%
+% Finally, the results of alignments which stored in |\gth@resq@x| and
+% |\gth@resq@y| are copied globally to the control sequences which stored in
+% |\gth@resulta| and |\gth@resultb|.
+% \begin{macrocode}
+ \expandafter\gth@glet\gth@resulta\gth@rseq@x
+ \expandafter\gth@glet\gth@resultb\gth@rseq@y}
+% \end{macrocode}
+% \end{macro}
+%
+% \subsection{Memoization Functions}\label{sect:memofunc}
+%
+% \begin{macro}{\gth@memo@ix}
+% \begin{macro}{\gth@memo@iy}
+% \begin{macro}{\gth@memo@m}
+% These are memoization functions for calculating $I^x, I^y, M$ respectively.
+% Since these functions change many `temporary' values, all of the processes
+% are wrapped in a group and only the return values and components of matrices
+% are assigned globally.
+% \begin{macrocode}
+\def\gth@memo@ix#1#2{%
+ \bgroup
+ \gth@tempcnta#1\gth@tempcntb#2\relax
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{\gth@sn @ix@\the\gth@tempcnta
+ @\the\gth@tempcntb}\relax
+ \advance\gth@tempcnta\m@ne
+ \gth@memo@ix{\gth@tempcnta}{\gth@tempcntb}%
+ \edef\gth@tmp@ix@return{\gth@ix@return}%
+ \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}%
+ \edef\gth@tmp@iy@return{\gth@iy@return}%
+ \gth@memo@m{\gth@tempcnta}{\gth@tempcntb}%
+ \advance\gth@tempcnta\@ne
+ \gth@advance{\gth@m@return}{-\gth@d}%
+ \gth@advance{\gth@tmp@ix@return}{-\gth@e}%
+ \gth@advance{\gth@tmp@iy@return}{-\gth@d}%
+ \gth@max{\gth@m@return,\gth@tmp@ix@return,\gth@tmp@iy@return}%
+ \gth@name@xdef{\gth@sn @ix@\the\gth@tempcnta
+ @\the\gth@tempcntb}{%
+ \the\gth@calc}%
+ \xdef\gth@ix@return{\the\gth@calc}
+ \else
+ \xdef\gth@ix@return{%
+ \gth@nameuse{\gth@sn @ix@\the\gth@tempcnta @\the\gth@tempcntb}}
+ \fi
+ \egroup}
+\def\gth@memo@iy#1#2{%
+ \bgroup
+ \gth@tempcnta#1\gth@tempcntb#2\relax
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{\gth@sn @iy@\the\gth@tempcnta
+ @\the\gth@tempcntb}\relax
+ \advance\gth@tempcntb\m@ne
+ \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}%
+ \edef\gth@tmp@iy@return{\gth@iy@return}%
+ \gth@memo@m{\gth@tempcnta}{\gth@tempcntb}%
+ \advance\gth@tempcntb\@ne
+ \gth@advance{\gth@m@return}{-\gth@d}%
+ \gth@advance{\gth@tmp@iy@return}{-\gth@e}%
+ \gth@max{\gth@m@return,\gth@tmp@iy@return}%
+ \gth@name@xdef{\gth@sn @iy@\the\gth@tempcnta
+ @\the\gth@tempcntb}{%
+ \the\gth@calc}%
+ \xdef\gth@iy@return{\the\gth@calc}%
+ \else
+ \xdef\gth@iy@return{%
+ \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}}
+ \fi
+ \egroup}
+\def\gth@memo@m#1#2{%
+ \bgroup
+ \gth@tempcnta#1\gth@tempcntb#2\relax
+ \expandafter\expandafter\expandafter
+ \ifx\gth@nameuse{\gth@sn @m@\the\gth@tempcnta
+ @\the\gth@tempcntb}\relax
+ \advance\gth@tempcnta\m@ne\advance\gth@tempcntb\m@ne
+ \gth@memo@ix{\gth@tempcnta}{\gth@tempcntb}%
+ \edef\gth@tmp@ix@return{\gth@ix@return}%
+ \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}%
+ \edef\gth@tmp@iy@return{\gth@iy@return}%
+ \gth@memo@m{\gth@tempcnta}{\gth@tempcntb}%
+ \edef\gth@tmpa{\gth@nameuse{seqa@\the\gth@tempcnta}}%
+ \edef\gth@tmpb{\gth@nameuse{seqb@\the\gth@tempcntb}}%
+ \advance\gth@tempcnta\@ne\advance\gth@tempcntb\@ne
+ \gth@max{\gth@m@return,\gth@tmp@ix@return,\gth@tmp@iy@return}%
+ \ifx\gth@tmpa\gth@tmpb
+ \advance\gth@calc\gth@match
+ \else
+ \advance\gth@calc\gth@mismatch
+ \fi
+ \gth@name@xdef{\gth@sn @m@\the\gth@tempcnta
+ @\the\gth@tempcntb}{%
+ \the\gth@calc}%
+ \xdef\gth@m@return{\the\gth@calc}%
+ \else
+ \xdef\gth@m@return{%
+ \gth@nameuse{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb}}%
+ \fi
+ \egroup}
+% \end{macrocode}
+% \end{macro}
+% \end{macro}
+% \end{macro}
+%
+% \subsection{Configuration Command}
+%
+% \begin{macro}{\GotohConfig}
+% This is just a wrap command of |\setkeys|.
+% \begin{macrocode}
+\newcommand{\GotohConfig}[1]{\setkeys[gth]{config}{#1}}
+% \end{macrocode}
+% \end{macro}
+%
+% \begin{thebibliography}{9}
+% \bibitem{flouri2015}
+% Flouri, Tom\'a\v s \textit{et al}., ``Are all global alignment
+% algorithms and implementations correct?''. \textit{bioRxiv}, 031500, 2015.
+% \bibitem{gotoh1982}
+% Gotoh, Osamu, ``An improved algorithm for matching biological sequences''.
+% \textit{Journal of Molecular Biology} \textbf{162}(3), 705-708, 1982.
+% \end{thebibliography}
+%
+% \Finale
+%
+\endinput
+% EOF
diff --git a/macros/latex/contrib/gotoh/gotoh.ins b/macros/latex/contrib/gotoh/gotoh.ins
new file mode 100644
index 0000000000..266c647389
--- /dev/null
+++ b/macros/latex/contrib/gotoh/gotoh.ins
@@ -0,0 +1,26 @@
+%%
+%% This is file `gotoh.ins'.
+%%
+%% Copyright (c) 2017 Takuto ASAKURA (wtsnjp)
+%% GitHub: https://github.com/wtsnjp
+%% Twitter: @wtsnjp
+%%
+%% This package is distributed under the MIT License.
+%%
+
+\input docstrip
+
+\preamble
+
+Copyright (c) 2017 Takuto ASAKURA (wtsnjp)
+ GitHub: https://github.com/wtsnjp
+ Twitter: @wtsnjp
+
+This package is distributed under the MIT License.
+
+\endpreamble
+
+\generate{\file{gotoh.sty}{\from{gotoh.dtx}{package}}}
+\endbatchfile
+
+%% EOF
diff --git a/macros/latex/contrib/gotoh/gotoh.pdf b/macros/latex/contrib/gotoh/gotoh.pdf
new file mode 100644
index 0000000000..1d0f526ced
--- /dev/null
+++ b/macros/latex/contrib/gotoh/gotoh.pdf
Binary files differ