Julien Y. Dutheil · Julien Y. Dutheil · Julien Y. Dutheil · 4fca7c1c · 4fca7c1c · 4fca7c1c
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ IF(NOT BUILD_STATIC)
      FORCE)
 ENDIF()
 IF(BUILD_STATIC)
-  MESSAGE("-- Static linkage requested.")
+  MESSAGE(STATUS "Static linkage requested.")
  SET (CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
 ENDIF()

@@ -50,7 +50,8 @@ else ()
  # Generate command line args (always add -c to output compressed file to stdout)
  if (${COMPRESS_PROGRAM} STREQUAL "gzip")
    # -n for no timestamp in files (reproducible builds)
-    set (COMPRESS_ARGS -c -n)
+    # -9 for maximum compression (lintian error)
+    set (COMPRESS_ARGS -c -n -9)
  else ()
    set (COMPRESS_ARGS -c)
  endif ()
@@ -152,10 +153,10 @@ ADD_SUBDIRECTORY(man)
 # Packager
 SET(CPACK_PACKAGE_NAME "maffilter")
 SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")
-SET(CPACK_PACKAGE_VERSION "1.3.0")
+SET(CPACK_PACKAGE_VERSION "1.3.1")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Filtering of genome alignment in the Multiple Alignment Format (MAF)")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")

--- a/MafFilter/MafFilter.cpp
+++ b/MafFilter/MafFilter.cpp
@@ -133,7 +133,7 @@ void help()
  (*ApplicationTools::message << "      ... param=option_file").endLine();
  (*ApplicationTools::message).endLine();
  (*ApplicationTools::message << "  Refer to the MafFilter Manual for a list of available options.").endLine();
-  (*ApplicationTools::message << "  Online version: http://biopp.univ-montp2.fr/manual/html/maffilter/").endLine();
+  (*ApplicationTools::message << "  Online version: https://jydu.github.io/maffilter/Manual/index.html").endLine();
  (*ApplicationTools::message << "  Or type 'info maffilter' in a terminal.").endLine();
  (*ApplicationTools::message << "__________________________________________________________________________").endLine();
 }
@@ -141,9 +141,9 @@ void help()
 int main(int args, char** argv)
 {
  cout << "******************************************************************" << endl;
-  cout << "*                  MAF Filter, version 1.3.0                     *" << endl;
+  cout << "*                  MAF Filter, version 1.3.1                     *" << endl;
  cout << "* Author: J. Dutheil                        Created on  10/09/10 *" << endl;
-  cout << "*                                           Last Modif. 09/03/18 *" << endl;
+  cout << "*                                           Last Modif. 18/08/18 *" << endl;
  cout << "******************************************************************" << endl;
  cout << endl;

@@ -1617,7 +1617,7 @@ int main(int args, char** argv)
        ApplicationTools::displayResult("-- Reference sequence", reference);
        
        bool map3 = ApplicationTools::getBooleanParameter("map3", cmdArgs, false);
-        ApplicationTools::displayBooleanResult("-- Ouput map3 file", map3);
+        ApplicationTools::displayBooleanResult("-- Output map3 file", map3);

        bool recodeChr = ApplicationTools::getBooleanParameter("recode_chr", cmdArgs, false);
        ApplicationTools::displayBooleanResult("-- Recode chromosomes", recodeChr);

--- a/buildBin.sh
+++ b/buildBin.sh
 #! /bin/sh
 arch=`uname -m`
-version=1.1.99-1
+version=1.3.0-1

 strip MafFilter/maffilter
 tar cvzf maffilter-${arch}-bin-static-${version}.tar.gz MafFilter/maffilter

--- a/debian/changelog
+++ b/debian/changelog
+maffilter (1.3.1+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version.
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Wed, 22 Aug 2018 11:39:47 +0200
+
 maffilter (1.3.0+dfsg-1) unstable; urgency=medium

  [ Steffen Moeller ]

--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
               cmake,
               texinfo,
-               libbpp-phyl-omics-dev (>= 2.4.0),
+               libbpp-phyl-omics-dev (>= 2.4.1),
               libboost-iostreams-dev (>= 1.54.0),
               zlib1g-dev,
               libbz2-dev

--- a/debian/patches/fix_doc_compression.patch
+++ b/debian/patches/fix_doc_compression.patch
-Author: Julien Y. Dutheil
-Last-Udpate: 2018-04-30 15:26:01 +0200
-Description: Maximum compression for documentation
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 2d4085b..0ee0c4d 100644
--- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -50,7 +50,8 @@ else ()
-   # Generate command line args (always add -c to output compressed file to stdout)
-   if (${COMPRESS_PROGRAM} STREQUAL "gzip")
-     # -n for no timestamp in files (reproducible builds)
-    set (COMPRESS_ARGS -c -n)
-+    # -9 for maximum compression (lintian error)
-+    set (COMPRESS_ARGS -c -n -9)
-   else ()
-     set (COMPRESS_ARGS -c)
-   endif ()
-
--- a/debian/patches/series
+++ b/debian/patches/series
-fix_doc_compression.patch
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -13,7 +13,7 @@ find_program (MAKEINFO NAMES makeinfo texi2any DOC "makeinfo doc generator progr
 if (NOT MAKEINFO)
  message (STATUS "makeinfo program not found: 'info' and 'html' target disabled (builds info/html doc)")
 else (NOT MAKEINFO)
-  message (STATUS "Found makeinfo as '${MAKEINFO}': 'info' and 'html' target enabled (builds info/html doc)")
+  message (STATUS "Found ${MAKEINFO}: 'info' and 'html' target enabled (builds info/html doc)")

  set (input ${CMAKE_CURRENT_SOURCE_DIR}/maffilter.texi)

@@ -58,6 +58,19 @@ else (NOT MAKEINFO)
    )
  add_custom_target (html DEPENDS ${output})

+  # Also provide a "html-multipages" target that builds html doc (not installed, and not part of "all").
+  set (output ${CMAKE_CURRENT_BINARY_DIR}/html/)
+  set (makeinfo-css "http://www.w3.org/StyleSheets/Core/Steely")
+  add_custom_command (
+    OUTPUT ${output}
+    COMMAND ${MAKEINFO} --html --no-headers --css-ref=${makeinfo-css} -o ${output} ${input}
+    DEPENDS ${input}
+    COMMENT "Generating html (multipages) doc"
+    VERBATIM
+    )
+  add_custom_target (html-multipages DEPENDS ${output})
+
+
  # Provide a "pdf" target that builds pdf doc (not installed, not part of "all").
  find_program (TEXIDVI NAMES texi2dvi)
  if (TEXIDVI)

--- a/doc/maffilter.texi
+++ b/doc/maffilter.texi
 \input texinfo   @c -*-texinfo-*-
 @c %**start of header
 @setfilename maffilter.info
-@settitle MafFilter Manual 1.3.0
+@settitle MafFilter Manual 1.3.1
 @c @documentencoding UTF-8
 @afourpaper
 @dircategory Science Biology Genetics
@@ -12,7 +12,7 @@


 @copying
-This is the manual of MafFilter, version 1.3.0.
+This is the manual of MafFilter, version 1.3.1.

 Copyright @copyright{} 2018 Julien Y. Dutheil
 @end copying

--- a/docs/Manual/AlnFilter.html
+++ b/docs/Manual/AlnFilter.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: AlnFilter</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: AlnFilter">
+<meta name="keywords" content="MafFilter Manual 1.3.1: AlnFilter">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Cleaning.html#Cleaning" rel="up" title="Cleaning">
+<link href="AlnFilter2.html#AlnFilter2" rel="next" title="AlnFilter2">
+<link href="RemoveEmptySequences.html#RemoveEmptySequences" rel="prev" title="RemoveEmptySequences">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="AlnFilter"></a>
+<div class="header">
+<p>
+Next: <a href="AlnFilter2.html#AlnFilter2" accesskey="n" rel="next">AlnFilter2</a>, Previous: <a href="RemoveEmptySequences.html#RemoveEmptySequences" accesskey="p" rel="prev">RemoveEmptySequences</a>, Up: <a href="Cleaning.html#Cleaning" accesskey="u" rel="up">Cleaning</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Alignment-filtering"></a>
+<h4 class="subsection">2.2.5 Alignment filtering</h4>
+
+<p>Split alignment blocks by removing regions with ambiguous alignments.
+The local uncertainty in the alignment is determined through a sliding window based approach.
+For each window, the number of gap characters and the total entropy are computed. Any window
+for which both the entropy and number of gaps exceed the given thresholds will be removed from
+the alignment, and the corresponding block split accordingly.
+</p>
+<a name="Synopsis_003a-13"></a>
+<h3 class="heading">Synopsis:</h3>
+
+<table class="cartouche" border="1"><tr><td>
+<div class="example">
+<pre class="example">maf.filter=                                 \
+    [...],
+    AlnFilter(                              \
+        species=(species1,species2,etc),    \
+        window.size=10,                     \
+        window.step=1,                      \
+        max.gap=9,                          \
+        max.ent=0.2,                        \
+        missing_as_gap=yes,                 \
+        relative=no,                        \
+        file=data.trash_aln.maf.gz,         \
+        compression=gzip),                  \
+    [...]
+</pre></div>
+</td></tr></table>
+
+<a name="Arguments_003a-12"></a>
+<h3 class="heading">Arguments:</h3>
+
+<dl compact="compact">
+<dt><code>species=(species1, species2, etc)</code></dt>
+<dd><p>A coma separated, within parentheses, list of species. All calculations will be performed on the sub-alignment corresponding to these species only.
+</p>
+</dd>
+<dt><code>window.size={int&gt;0}</code></dt>
+<dd><p>The width, in bp, of the sliding window.
+</p>
+</dd>
+<dt><code>window.step={int&gt;0}</code></dt>
+<dd><p>The step by which the window is moved, in bp.
+</p>
+</dd>
+<dt><code>relative={boolean}</code></dt>
+<dd><p>Tell if maximum amount of gap is relative (that is, as a proportion of the total amount of character in each window).
+</p>
+</dd>
+<dt><code>max.gap={int&gt;0|1&gt;double&gt;0}</code></dt>
+<dd><p>The maximum number of gaps allowed in each window (if relative is set to no), or the maximum proportion of gaps (if relative is set to yes)
+</p>
+</dd>
+<dt><code>max.ent={float}</code></dt>
+<dd><p>The maximum entropy allowed in each window.
+</p>
+</dd>
+<dt><code>missing_as_gap={yes/no}</code></dt>
+<dd><p>Tell if missing sequences should be considered as gaps.
+</p>
+</dd>
+<dt><code>file={none|{path}}</code></dt>
+<dd><p>An optional file were removed alignment parts will be stored, in the MAF format.
+This can be helpful for visual inspection and fine tuning of the filter parameters.
+</p>
+</dd>
+<dt><code>compression={none|gzip|zip|bzip2}</code></dt>
+<dd><p>Compression format for output file (if file != none).
+</p>
+</dd>
+</dl>
+
+
+
+
+
+</body>
+</html>
--- a/docs/Manual/AlnFilter2.html
+++ b/docs/Manual/AlnFilter2.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: AlnFilter2</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: AlnFilter2">
+<meta name="keywords" content="MafFilter Manual 1.3.1: AlnFilter2">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Cleaning.html#Cleaning" rel="up" title="Cleaning">
+<link href="EntropyFilter.html#EntropyFilter" rel="next" title="EntropyFilter">
+<link href="AlnFilter.html#AlnFilter" rel="prev" title="AlnFilter">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="AlnFilter2"></a>
+<div class="header">
+<p>
+Next: <a href="EntropyFilter.html#EntropyFilter" accesskey="n" rel="next">EntropyFilter</a>, Previous: <a href="AlnFilter.html#AlnFilter" accesskey="p" rel="prev">AlnFilter</a>, Up: <a href="Cleaning.html#Cleaning" accesskey="u" rel="up">Cleaning</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Alignment-filtering-2"></a>
+<h4 class="subsection">2.2.6 Alignment filtering 2</h4>
+
+<p>This is another algorithm for cleaning alignment blocks (see AlnFilter), using sliding windows.
+The number of gaps in each alignment column in the window is counted, and the column is masked if it contains more than a given threshold of gaps. consecutive patterns in the window are only counted ones. In the follwing 10nt window:
+</p><pre class="verbatim">AATCGGGCGT
+AA---GCGGA
+AA---CGGGT
+CA---CGGGA
+</pre><p>positions 3, 4 and 5 will be masked if the maximum number of gaps allowed is 2 or less. The three columns will however count as only one indel event.
+The window is then discarded if it contains more than a given number of indel events.
+</p>
+<a name="Synopsis_003a-14"></a>
+<h3 class="heading">Synopsis:</h3>
+
+<table class="cartouche" border="1"><tr><td>
+<div class="example">
+<pre class="example">maf.filter=                                 \
+    [...],
+    AlnFilter2(                             \
+        species=(species1,species2,etc),    \
+        window.size=10,                     \
+        window.step=1,                      \
+        max.gap=1,                          \
+        max.pos=1,                          \
+        relative=no,                        \
+        missing_as_gap=yes,                 \
+        file=data.trash_aln.maf.gz,         \
+        compression=gzip),                  \
+    [...]
+</pre></div>
+</td></tr></table>
+
+<a name="Arguments_003a-13"></a>
+<h3 class="heading">Arguments:</h3>
+
+<dl compact="compact">
+<dt><code>species=(species1, species2, etc)</code></dt>
+<dd><p>A coma separated, within parentheses, list of species. All calculations will be performed on the sub-alignment corresponding to these species only.
+</p>
+</dd>
+<dt><code>window.size={int&gt;0}</code></dt>
+<dd><p>The width, in bp, of the sliding window.
+</p>
+</dd>
+<dt><code>window.step={int&gt;0}</code></dt>
+<dd><p>The step by which the window is moved, in bp.
+</p>
+</dd>
+<dt><code>relative={boolean}</code></dt>
+<dd><p>Tell if maximum amount of gap is relative (that is, as a proportion of the total amount of character in each site).
+</p>
+</dd>
+<dt><code>max.gap={int&gt;0|1&gt;double&gt;0}</code></dt>
+<dd><p>The maximum number of gaps allowed in each site (if relative is set to no), or the maximum proportion of gaps (if relative is set to yes)
+</p>
+</dd>
+<dt><code>max.pos={int&gt;0}</code></dt>
+<dd><p>The maximum number of positions with gaps (&ldquo;indel events&rdquo;).
+</p>
+</dd>
+<dt><code>missing_as_gap={yes/no}</code></dt>
+<dd><p>Tell if missing sequences should be considered as gaps.
+</p>
+</dd>
+<dt><code>file={none|{path}}</code></dt>
+<dd><p>An optional file were removed alignment parts will be stored, in the MAF format.
+This can be helpful for visual inspection and fine tuning of the filter parameters.
+</p>
+</dd>
+<dt><code>compression={none|gzip|zip|bzip2}</code></dt>
+<dd><p>Compression format for output file (if file != none).
+</p>
+</dd>
+</dl>
+
+
+
+
+
+</body>
+</html>
--- a/docs/Manual/AlnScore.html
+++ b/docs/Manual/AlnScore.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: AlnScore</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: AlnScore">
+<meta name="keywords" content="MafFilter Manual 1.3.1: AlnScore">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
+<link href="BlockCounts.html#BlockCounts" rel="next" title="BlockCounts">
+<link href="SequenceLength.html#SequenceLength" rel="prev" title="SequenceLength">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="AlnScore"></a>
+<div class="header">
+<p>
+Next: <a href="BlockCounts.html#BlockCounts" accesskey="n" rel="next">BlockCounts</a>, Previous: <a href="SequenceLength.html#SequenceLength" accesskey="p" rel="prev">SequenceLength</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Alignment-score"></a>
+<h4 class="subsubsection">2.3.1.4 Alignment score</h4>
+<p>The <code>AlnScore</code> statistics reports the alignment score associated to the block, if any.
+</p>
+<p>(No argument)
+</p>
+
+
+
+</body>
+</html>
--- a/docs/Manual/Analyzing.html
+++ b/docs/Manual/Analyzing.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: Analyzing</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: Analyzing">
+<meta name="keywords" content="MafFilter Manual 1.3.1: Analyzing">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Filters.html#Filters" rel="up" title="Filters">
+<link href="Descriptive.html#Descriptive" rel="next" title="Descriptive">
+<link href="FeatureFilter.html#FeatureFilter" rel="prev" title="FeatureFilter">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="Analyzing"></a>
+<div class="header">
+<p>
+Next: <a href="Exporting.html#Exporting" accesskey="n" rel="next">Exporting</a>, Previous: <a href="Cleaning.html#Cleaning" accesskey="p" rel="prev">Cleaning</a>, Up: <a href="Filters.html#Filters" accesskey="u" rel="up">Filters</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Statistical-analysis"></a>
+<h3 class="section">2.3 Statistical analysis</h3>
+
+
+
+
+
+</body>
+</html>
--- a/docs/Manual/BlockCounts.html
+++ b/docs/Manual/BlockCounts.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: BlockCounts</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: BlockCounts">
+<meta name="keywords" content="MafFilter Manual 1.3.1: BlockCounts">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
+<link href="PairwiseDivergence.html#PairwiseDivergence" rel="next" title="PairwiseDivergence">
+<link href="AlnScore.html#AlnScore" rel="prev" title="AlnScore">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="BlockCounts"></a>
+<div class="header">
+<p>
+Next: <a href="PairwiseDivergence.html#PairwiseDivergence" accesskey="n" rel="next">PairwiseDivergence</a>, Previous: <a href="AlnScore.html#AlnScore" accesskey="p" rel="prev">AlnScore</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Character-frequencies"></a>
+<h4 class="subsubsection">2.3.1.5 Character frequencies</h4>
+<p>The <code>BlockCounts</code> statistics reports the count of each character found in the block.
+</p>
+<p>Note: this statistics does not work in case of duplicated sequences (multiple hits from the same chromosome / scaffold / contig).
+</p>
+<a name="Arguments_003a-20"></a>
+<h3 class="heading">Arguments:</h3>
+<dl compact="compact">
+<dt><code>species={list}</code></dt>
+<dd><p>A list of species to be considered in the counts calculations. If no species is given, all sequences are used.
+</p></dd>
+<dt><code>suffix={string}</code></dt>
+<dd><p>An (optional) suffix to append to the statistics name. Useful in case the statistics should be computed for several species independently.
+</p></dd>
+</dl>
+
+
+
+
+</body>
+</html>
--- a/docs/Manual/BlockLength.html
+++ b/docs/Manual/BlockLength.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: BlockLength</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: BlockLength">
+<meta name="keywords" content="MafFilter Manual 1.3.1: BlockLength">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
+<link href="SequenceLength.html#SequenceLength" rel="next" title="SequenceLength">
+<link href="BlockSize.html#BlockSize" rel="prev" title="BlockSize">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="BlockLength"></a>
+<div class="header">
+<p>
+Next: <a href="SequenceLength.html#SequenceLength" accesskey="n" rel="next">SequenceLength</a>, Previous: <a href="BlockSize.html#BlockSize" accesskey="p" rel="prev">BlockSize</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Length-of-alignment-blocks"></a>
+<h4 class="subsubsection">2.3.1.2 Length of alignment blocks</h4>
+<p>The <code>BlockLength</code> statistics reports the number of sites in the block.
+</p>
+<p>(No argument)
+</p>
+
+
+
+</body>
+</html>
--- a/docs/Manual/BlockSize.html
+++ b/docs/Manual/BlockSize.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: BlockSize</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: BlockSize">
+<meta name="keywords" content="MafFilter Manual 1.3.1: BlockSize">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
+<link href="BlockLength.html#BlockLength" rel="next" title="BlockLength">
+<link href="Descriptive.html#Descriptive" rel="prev" title="Descriptive">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="BlockSize"></a>
+<div class="header">
+<p>
+Next: <a href="BlockLength.html#BlockLength" accesskey="n" rel="next">BlockLength</a>, Previous: <a href="Descriptive.html#Descriptive" accesskey="p" rel="prev">Descriptive</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Size-of-alignment-blocks"></a>
+<h4 class="subsubsection">2.3.1.1 Size of alignment blocks</h4>
+<p>The <code>BlockSize</code> statistics reports the number of sequences in the block.
+</p>
+<p>(No argument)
+</p>
+
+
+
+</body>
+</html>
--- a/docs/Manual/Cleaning.html
+++ b/docs/Manual/Cleaning.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: Cleaning</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: Cleaning">
+<meta name="keywords" content="MafFilter Manual 1.3.1: Cleaning">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Filters.html#Filters" rel="up" title="Filters">
+<link href="MinBlockLength.html#MinBlockLength" rel="next" title="MinBlockLength">
+<link href="WindowSplit.html#WindowSplit" rel="prev" title="WindowSplit">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="Cleaning"></a>
+<div class="header">
+<p>
+Next: <a href="Analyzing.html#Analyzing" accesskey="n" rel="next">Analyzing</a>, Previous: <a href="Extracting.html#Extracting" accesskey="p" rel="prev">Extracting</a>, Up: <a href="Filters.html#Filters" accesskey="u" rel="up">Filters</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Cleaning-alignment-blocks"></a>
+<h3 class="section">2.2 Cleaning alignment blocks</h3>
+
+
+
+
+
+
+</body>
+</html>
--- a/docs/Manual/Concatenate.html
+++ b/docs/Manual/Concatenate.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: Concatenate</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: Concatenate">
+<meta name="keywords" content="MafFilter Manual 1.3.1: Concatenate">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Extracting.html#Extracting" rel="up" title="Extracting">
+<link href="OrderFilter.html#OrderFilter" rel="next" title="OrderFilter">
+<link href="Merge.html#Merge" rel="prev" title="Merge">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="Concatenate"></a>
+<div class="header">
+<p>
+Next: <a href="OrderFilter.html#OrderFilter" accesskey="n" rel="next">OrderFilter</a>, Previous: <a href="Merge.html#Merge" accesskey="p" rel="prev">Merge</a>, Up: <a href="Extracting.html#Extracting" accesskey="u" rel="up">Extracting</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Concatenating_003a-merge-consecutive-blocks-up-to-a-certain-size"></a>
+<h4 class="subsection">2.1.4 Concatenating: merge consecutive blocks up to a certain size</h4>
+
+<p>The <code>Concatenate</code> filter fuses consecutive blocks until the concatenated block reaches a minimal size.
+</p>
+<a name="Synopsis_003a-4"></a>
+<h3 class="heading">Synopsis:</h3>
+
+<table class="cartouche" border="1"><tr><td>
+<div class="example">
+<pre class="example">maf.filter=                                 \
+    [...],
+    Concatenate(minimum_size=10000, ref_species=Hsapiens), \
+    [...]
+</pre></div>
+</td></tr></table>
+
+<a name="Arguments_003a-3"></a>
+<h3 class="heading">Arguments:</h3>
+
+<dl compact="compact">
+<dt><code>minimum_size={int}</code></dt>
+<dd><p>The minimum size for the blocks to be reached.
+</p>
+</dd>
+<dt><code>ref_species={string}</code></dt>
+<dd><p>If given, only blocks with identical chromosome tags in the reference species will be merged.
+</p>
+</dd>
+</dl>
+
+
+
+
+
+</body>
+</html>
--- a/docs/Manual/CountClusters.html
+++ b/docs/Manual/CountClusters.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: CountClusters</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: CountClusters">
+<meta name="keywords" content="MafFilter Manual 1.3.1: CountClusters">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Descriptive.html#Descriptive" rel="up" title="Descriptive">
+<link href="ModelFit.html#ModelFit" rel="next" title="ModelFit">
+<link href="DiversityStatistics.html#DiversityStatistics" rel="prev" title="DiversityStatistics">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="CountClusters"></a>
+<div class="header">
+<p>
+Next: <a href="ModelFit.html#ModelFit" accesskey="n" rel="next">ModelFit</a>, Previous: <a href="DiversityStatistics.html#DiversityStatistics" accesskey="p" rel="prev">DiversityStatistics</a>, Up: <a href="Descriptive.html#Descriptive" accesskey="u" rel="up">Descriptive</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Number-of-sequence-clusters_002e"></a>
+<h4 class="subsubsection">2.3.1.12 Number of sequence clusters.</h4>
+<p><code>CountClusters</code> counts the number of sequence clusters. This requires that a clustering tree was previously computed (see below).
+</p>
+<a name="Synopsis_003a-27"></a>
+<h3 class="heading">Synopsis:</h3>
+
+<table class="cartouche" border="1"><tr><td>
+<div class="example">
+<pre class="example">maf.filter=                                 \
+    [...],                                   
+    SequenceStatistics(                     \
+        statistics=(\                       \
+            [...],                                                    
+            CountClusters(                  \
+                tree=bionj,                 \
+                threshold=0.001),           \
+            [...]),                         \
+        ref_species=species1,               \
+        file=data.statistics.csv),          \
+    [...]
+</pre></div>
+</td></tr></table>
+
+<a name="Arguments_003a-27"></a>
+<h3 class="heading">Arguments:</h3>
+<dl compact="compact">
+<dt><code>tree={string}</code></dt>
+<dd><p>The tag name used to store the previously computed tree.
+</p>
+</dd>
+<dt><code>threshold={double}</code></dt>
+<dd><p>The threshold to use in order to compute clusters. A threshold of 0.001 for instance means that sequences within each cluster will be divergent by maximum 0.001, while sequences in distinct clusters will be divergent by at least 0.001.
+</p> 
+</dd>
+</dl>
+
+
+
+
+
+</body>
+</html>
--- a/docs/Manual/Description.html
+++ b/docs/Manual/Description.html
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<!-- This is the manual of MafFilter, version 1.3.1.
+
+Copyright (C) 2018 Julien Y. Dutheil -->
+<!-- Created by GNU Texinfo 6.1, http://www.gnu.org/software/texinfo/ -->
+<head>
+<title>MafFilter Manual 1.3.1: Description</title>
+
+<meta name="description" content="MafFilter Manual 1.3.1: Description">
+<meta name="keywords" content="MafFilter Manual 1.3.1: Description">
+<meta name="resource-type" content="document">
+<meta name="distribution" content="global">
+<meta name="Generator" content="makeinfo">
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link href="index.html#Top" rel="start" title="Top">
+<link href="index.html#SEC_Contents" rel="contents" title="Table of Contents">
+<link href="Introduction.html#Introduction" rel="up" title="Introduction">
+<link href="Run.html#Run" rel="next" title="Run">
+<link href="Introduction.html#Introduction" rel="prev" title="Introduction">
+<style type="text/css">
+<!--
+a.summary-letter {text-decoration: none}
+blockquote.indentedblock {margin-right: 0em}
+blockquote.smallindentedblock {margin-right: 0em; font-size: smaller}
+blockquote.smallquotation {font-size: smaller}
+div.display {margin-left: 3.2em}
+div.example {margin-left: 3.2em}
+div.lisp {margin-left: 3.2em}
+div.smalldisplay {margin-left: 3.2em}
+div.smallexample {margin-left: 3.2em}
+div.smalllisp {margin-left: 3.2em}
+kbd {font-style: oblique}
+pre.display {font-family: inherit}
+pre.format {font-family: inherit}
+pre.menu-comment {font-family: serif}
+pre.menu-preformatted {font-family: serif}
+pre.smalldisplay {font-family: inherit; font-size: smaller}
+pre.smallexample {font-size: smaller}
+pre.smallformat {font-family: inherit; font-size: smaller}
+pre.smalllisp {font-size: smaller}
+span.nolinebreak {white-space: nowrap}
+span.roman {font-family: initial; font-weight: normal}
+span.sansserif {font-family: sans-serif; font-weight: normal}
+ul.no-bullet {list-style: none}
+-->
+</style>
+<link rel="stylesheet" type="text/css" href="http://www.w3.org/StyleSheets/Core/Steely">
+
+
+</head>
+
+<body lang="en">
+<a name="Description"></a>
+<div class="header">
+<p>
+Next: <a href="Run.html#Run" accesskey="n" rel="next">Run</a>, Previous: <a href="Introduction.html#Introduction" accesskey="p" rel="prev">Introduction</a>, Up: <a href="Introduction.html#Introduction" accesskey="u" rel="up">Introduction</a> &nbsp; [<a href="index.html#SEC_Contents" title="Table of contents" rel="contents">Contents</a>]</p>
+</div>
+<a name="Description-of-the-program"></a>
+<h3 class="section">1.1 Description of the program</h3>
+
+<p>The main goal of MafFilter is to apply a series of &quot;filters&quot; to the original input file.
+A &ldquo;filter&rdquo; can be seen as a small program that takes as input one or several maf blocks, and outputs one or several maf block, after performing some actions on them:
+</p>
+<pre class="verbatim">                         +--------+
+   Alignment block(s)    |        |   Alignment block(s)
+------------------------&gt;+ Filter +------------------------&gt;
+                         |        |
+                         +--------+
+</pre>
+<p>We can roughly distinguish four types of filters:
+</p>
+<ul>
+<li> Filters that take one block as input, and output one single block, possibly after removing some sequences, or even the full block if it did not match a certain criterion,
+</li><li> Filters that take one block as input, and split them into several smaller blocks, for instance of a fixed size,
+</li><li> Filters that take several blocks as input and output a larger one, typically after concatenating the input blocks,
+</li><li> Filters that do not modify the input block and simply forward it, yet after having performed some computations, for instance calculating various statistics.
+</li></ul>
+
+<p>A run of MafFilter typically consists in a workflow of filters, applied in a serial way, the output of one filter being taken as input as the next one.
+In the current version of MafFilter, only linear workflows are possible, without branching:
+</p>
+<pre class="verbatim">    +----------+    +----------+    +----------+
+    |          |    |          |    |          |
+---&gt;+ Filter 1 +---&gt;+ Filter 2 +---&gt;+ Filter 3 +---&gt; Etc.
+    |          |    |          |    |          |
+    +----------+    +----------+    +----------+
+</pre>
+<p>Branching processes can however be achieved by outputing the alignment blocks at the branching point, and run various instances of MafFilter on the resulting files:
+</p>
+<pre class="verbatim">     Run 1
+    +----------+    +----------+    +----------+
+    |          |    |          |    |          |
+---&gt;+ Filter 1 +---&gt;+ Filter 2 +---&gt;+ Filter 3 +---&gt; Etc.
+    |          |    |          |    |          |
+    +----------+    +----+-----+    +----------+
+                         |
+                         |    +------------+
+                         |    |            |
+     Run 2               +---&gt;+ Filter 2.1 +---&gt; Etc.
+                              |            |
+                              +------------+
+</pre>
+<p>Some filters allow to generate additional data associated to each alignment block, such as phylogenetic trees.
+Such data cannot be written to file together with the blocks, as the MAF format does not support this.
+These data are however stored in memory by MafFilter together with the block, as &ldquo;extra-data&rdquo;.
+Extra-data are associated with a special tag which is used for refering to them, including for writting them in appropriate output files.
+</p>
+<p>The next section describes how to specify the series of filters to be applied, and the next chapter provides an exhaustive list of available filters.
+</p>
+
+
+
+
+</body>
+</html>