Benjamin Redelings · Benjamin Redelings · Benjamin Redelings · Benjamin Redelings · Benjamin Redelings · 8aef941b
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -15,7 +15,7 @@ install:

 build_script:
  - bash -lc "cd $APPVEYOR_BUILD_FOLDER/ && git submodule update --init"
-  - bash -lc "cd $APPVEYOR_BUILD_FOLDER/ && meson.py build --prefix=$APPVEYOR_BUILD_FOLDER/local"
+  - bash -lc "cd $APPVEYOR_BUILD_FOLDER/ && meson build --prefix=$APPVEYOR_BUILD_FOLDER/local"
  - bash -lc "cd $APPVEYOR_BUILD_FOLDER/build && ninja install
 #  - bash -lc "cd $APPVEYOR_BUILD_FOLDER/build && ninja test"


--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@ doc/html
 doc/latex
 \#*#
 *.orig
+build*/
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,37 +5,37 @@ language: cpp
 matrix:
  include:
    - os: linux
-      dist: trusty
-      env: CXX_COMPILER=g++-5
+      dist: xenial
+      env: CXX_COMPILER=g++-6
      addons:
        apt:
          sources:
          - ubuntu-toolchain-r-test
          packages:
-          - g++-5
+          - g++-6
          - pandoc
    - os: linux
-      dist: trusty
-      env: CXX_COMPILER=g++-6
+      dist: xenial
+      env: CXX_COMPILER=g++-7
      addons:
        apt:
          sources:
          - ubuntu-toolchain-r-test
          packages:
-          - g++-6
+          - g++-7
          - pandoc
    - os: linux
-      dist: trusty
-      env: CXX_COMPILER=g++-7
+      dist: xenial
+      env: CXX_COMPILER=g++-8
      addons:
        apt:
          sources:
          - ubuntu-toolchain-r-test
          packages:
-          - g++-7
+          - g++-8
          - pandoc
    - os: linux
-      dist: trusty
+      dist: xenial
      compiler: clang++
      addons:
        apt:
@@ -44,12 +44,12 @@ matrix:
          packages:
          - g++-7
          - pandoc
+    - os: osx
+      osx_image: xcode10.1
    - os: osx
      osx_image: xcode9.2
    - os: osx
      osx_image: xcode8.3
-    - os: osx
-      osx_image: xcode7.3

 before_install:
  # We need to re-export CC and CXX here, because travis exports CXX=g++ or clang++ AFTER we set CXX.

--- a/NEWS
+++ b/NEWS
-UNRELEASED
+* 3.4 (Dec 13, 2018)
+ - Evolutionary models
+   - Add Doublet alphabet for RNA stems.
+   - Add generic +mut_sel model modifier.
+   + Add models x2, x2_sym, x2x2 for RNA stems.
+   + Add RNA.m16a model for RNA stems.
 - Fixes
- - 
+   - "--" should not become a single long dash (en-dash) in man pages.
+   + Don't crash if --scale is set to a constant (e.g. --scale=1).
+   - Allow reading (a,b):1.0; by ignoring the root branch length.
+   + Properly translate newick labels with quotes or _.
+   + Don't replace W with A in observed sequences unless --set infer-ambiguous-observed=true
+ - Misc
+   - Correctly log things inside a let binding.
+   + Allow selecting character ranges from a file: "sequences.fasta:100-240,300-900"
+   + Rename subsample to bali-subsample (to avoid conflicts with other software).
+   + Install bali-phy-pkg.
+   + Make BES package work again.
+   + Reorganize fields on C1.log
+   - Hold Numeric[k] or Doublets[DNA/RNA] alignments fixed.
+   - Allow writing alignments every iteration.
+   - tree-tool: add scaling, pruning, computing diameter, etc.
+   - cut-range: allow selection samples from more than 1 alignment file
+   - alignment-thin: clean up options and man page.
+   - alignment-distances: new tool, add accuracy and recall metrics.
+ - MCMC
+   - Only compute probability *ratios*
+     + Allow recovery from initial -infinity.
+   - Improved mixing for [0,1] random variables.
+ - Graphical model framework
+   - Interpreted models now separate the likelihood from the prior in logged output.
+   - Interpreted models (e.g. LinearRegression.hs) are now a lot faster.
+   - Simplify constructing loggers.
+   - Allow using poisson distribution.
+ - Haskell
+   - Allow "import modid ( .... )" and "import modid hiding ( .... )"
+   - Add Data.JSON module
+   - Implement quot, rem, div, mod.
+   - Implement -X NoImplicitPrelude
+   - Refactored functions out of Prelude into Data.List, etc.
+   - Implement layout-sensitive parsing.
+   - Implement pattern bindings (i.e. let (x,y) = E1 in E2)
+   - Implement @-patterns (i.e. x@(y,z) )
+   - Implement lazy patterns (i.e. ~(y,z)  )
+   - Implement guards for functions and case.
+   - Allow modules with no "module Name where" clause.
+   - Implement running a module with --run-module
+   - Encode strings as (listFromString String)
+   - Add flags for dumping parsed, renamed, desugared, etc. code.
+   - [FIX] float let out of let if it reveals a constant.

 * 3.3 (Aug 6, 2018)
  - Fixes
@@ -15,7 +62,7 @@ UNRELEASED
    - add gy94_ext and mg94_ext for using any nucleotide rate matrix.
    - add mg94k for mg94_ext[hky85]
  - Triplet models
-    - fix up x3, x3_xym, x3x3
+    - fix up x3, x3_sym, x3x3
    - add +dNdS function so we can do e.g. hky85+x3+dNdS
  - Functions in models
    - Add new syntax function[x,...] for specifying models.
@@ -144,7 +191,7 @@ UNRELEASED
  * Read json using nlohmann::json
  * Switch to new ptree structure.

-3.0-beta5 (Dec 6, 2018)
+3.0-beta5 (Dec 6, 2017)
  - Fixes
    - Don't crash on --smodel=GTR+x3
  - Short parameter names

--- a/README.md
+++ b/README.md
@@ -57,12 +57,10 @@ Build BAli-Phy
 --------------
 ```
 git clone https://github.com/bredelings/BAli-Phy.git
-cd BAli-Phy/
-git submodule update --init   # This is optional, it allows running the testiphy testsuite
-
+cd BAli-Phy
 meson build --prefix=$HOME/Applications/bali-phy
-ninja -C install
-ninja -C test
+ninja -C build install
+ninja -C build test
 ```

 Adding bali-phy to your `$PATH`

--- a/debian/changelog
+++ b/debian/changelog
+bali-phy (3.4+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Remove patches applied upstream.
+  * Update to Standards-Version 4.2.1
+
+ -- Benjamin Redelings <benjamin.redelings@gmail.com>  Thu, 13 Dec 2018 20:56:16 -0500
+
 bali-phy (3.3+dfsg-1) unstable; urgency=medium

  * New upstream version

--- a/debian/control
+++ b/debian/control
@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 11),
               libboost-system-dev,
               libboost-filesystem-dev,
               libboost-chrono-dev
-Standards-Version: 4.1.5
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/bali-phy
 Vcs-Git: https://salsa.debian.org/med-team/bali-phy.git
 Homepage: http://www.bali-phy.org

--- a/debian/patches/series
+++ b/debian/patches/series
-test-python3
--- a/debian/patches/test-python3
+++ b/debian/patches/test-python3
-Author: Benjamin Redelings
-Last-Update: 2018-05-06 07:50:25 -0400
-Description: Run tests by explicitly unsing Python3
-
-Index: bali-phy/tests/run-tests.py
-===================================================================
--- bali-phy.orig/tests/run-tests.py
-+++ bali-phy/tests/run-tests.py
-@@ -1,4 +1,4 @@
-#!/usr/bin/python
-+#!/usr/bin/python3
- from __future__ import print_function
- import subprocess
- import os
--- a/doc/NEWS
+++ b/doc/NEWS
-Changes in 1.8.17
- * [BUGFIX] Make sure proposals and priors are on the same scale.
- * [BUGFIX] We MUST sample both nodes and alignment in SPR moves.
- * [NEW]    Add some documentation.
- * [NEW]    Make tool 'tree-dist-compare' compare any number of 
-            tree distributions.
- * [CHANGE] Increase mixing for epsilon...
- * [CHANGE] Sanitize the interface.
- * [CHANGE] Make the makefile self-contained.
- * [CHANGE] Introduce shift_laplace prior to allow data to overpower
-            prior.  Use in prior on kappa + omega.
-
-Changes in 1.8.13:
- * [BUGFIX] Our branch length proposal was biased upwards! Fixed.
- * [CHANGE] Sanitize move attributes
- * [CHANGE] Make 'gaps=star' automatically disable conflicting moves.
- * [CHANGE] Print out weights
- * [DEBUG]  In debug mode, check that our cached transition matrices
-            are correct.
-
-Changes in 1.8.12:
- * [BUGFIX] Make tree operator=(*this) do nothing.
- * Store partial emission probabilities in Matrix instead of vector<
-   valarray<double> >.
- * Compute and cache emission probabilities e(i,j)
- * Alter s2_sub to reduce the number of operations needed to compute
-   e(i,j)
-
-Changes in 1.8.11:
- * Compute GQ probabilities using new State-Reduction (SR) algorithm
- * Add new routine logdiff(x,y) = log(exp(x)-exp(y))
- * Unify several routines to just call sample_two_nodes_multi()
- * Unify several routines to just call sample_tri_multi()
-
-Changes in 1.8.9:
- * Change the name 'sampler' to 'bali-phy'.
- * [CHANGE] Further improve and unify loading of alignments w/ and w/o
-            internal nodes.
- * [CHANGE] Update alignment-blame and make it run again
- * [CHANGE] Check that target matches samples!
- * Put debugging output from optimize.C under #ifndef NDEBUG
- * [CHANGE] Don't complain about missing letters while trying to
-            determine the alphabet.
- * [BUGFIX] Fix tree_sample::supports_topology when topology NEVER
-   occurs
-
-Changes in 1.8.8: 
- * [FEATURE] Change randomize_alignment to be useable with large
-             number of taxa.
- * [BUGFIX] Change topology branch score by factor of 2
- * [CHANGE] Make alignments print only every 10 iterations to decrease
-            file size.
- * [CHANGE] Improve and unify loading of alignments w/ and w/o
-            internal nodes
- * [CHANGE] Check that internal node states are not letters, and are
-            consistent when loading alignments.
- * [CHANGE] Change mode of kappa distribution to 2, and increase
-            variance.
- * [CHANGE] Change kappa initial value to 2.
- * [CHANGE] Improve tree-dist-compare
- * move calculations of likelihoods on half-trees to alignment-sums.C
- * remove move slide_branch_and_T
- * break off part of class HMM into class DPengine
- * break off part of hmm.H into dp-engine.H
- * remove TreeFunc - it wasn't really used
-
-Changes in 1.8.7:
- * [FEATURE] Throw an exception if we set a parameters twice on the
-             command line 
- * [FEATURE] New tool tree-dist-compare.C, new file tree-dist.C
- * [BUGFIX]  We accidentally changed SPR_and_A to SPR_and_nodes in
-             1.8.6. Change it back! 
- * [BUGFIX] Correctly print the branch length for the highest numbered
-            branch.
- * [BUGFIX] The "branch score" distance was broken
-
-Changes in 1.8.6
- * [BUGFIX] remember to recalc() the branches that SPR changes!
- * [CHANGE] Change branch_mean proposals to log scale
- * [CHANGE] Change kappa,omega proposals to log scale in HKY and
-            YangCodonModel.
-
-
-Changes in 1.8.5:
- * [BUGFIX] Con't crash when a MCMC MoveEach has no enabled moves
-            for an arg.  Instead, assert.
- * [CHANGE] Run the tree moves twice every iteration....
- * [CHANGE] Run SPR more often
\ No newline at end of file
--- a/doc/README.html
+++ b/doc/README.html
--- a/doc/README.itex.xml
+++ b/doc/README.itex.xml
--- a/doc/README.pdf
+++ b/doc/README.pdf
--- a/doc/README.xhtml
+++ b/doc/README.xhtml
--- a/doc/Tutorial4.tut.xml
+++ b/doc/Tutorial4.tut.xml
@@ -15,8 +15,17 @@
  </info>

  <section xml:id="intro"><info><title>Introduction</title></info>
+  <para>This tutorial offers a quick overview of bali-phy with an emphasis on concrete analysis of real datasets.  Other documentation includes:
+  <itemizedlist>
+    <listitem>The <link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.bali-phy.org/README.xhtml">Users Guide</link> is much more complete.</listitem>
+    <listitem>Run <userinput><replaceable>tool</replaceable> --help</userinput> to see command line options for <replaceable>tool</replaceable>.</listitem>
+    <listitem>Run <userinput>man <replaceable>tool</replaceable></userinput> to see the manual page for <replaceable>tool</replaceable>.</listitem>
+    <listitem>Manual pages for bali-phy and tools are also available <link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.bali-phy.org/docs.php#manpages">online</link>.</listitem>
+  </itemizedlist>
+  </para>
+
 <para>
-Before you start this tutorial, please <link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.bali-phy.org/download.php">download</link> and install bali-phy, following the installation instructions in the <link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.bali-phy.org/README.html">manual</link>.</para>
+Before you start this tutorial, please <link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.bali-phy.org/download.php">download</link> and install bali-phy, following the installation instructions in the <link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.bali-phy.org/README.html">User Guide</link>.</para>
  </section>
  <section xml:id="work_directory"><info><title>Setting up the <filename>~/alignment_files</filename> directory</title></info>

@@ -50,22 +59,34 @@ What version of bali-phy are you running?  When was it compiled?  Which compiler
 Look at the list of command line options:
 % bali-phy -h     | less
 % bali-phy --help | less
-As you can see, many options have a long form, and a short form which is a single letter.
+% bali-phy help   | less
+By default, not all the options are shown.  To see more options, try:
+% bali-phy help advanced | less
+% bali-phy help expert   | less
+</para>
+<para>All bali-phy tools also take <userinput>--help</userinput>.
+% alignment-thin --help | less
+% alignment-cat --help  | less
 </para>
+</section>
+
+<section xml:id="help"><info><title>Help</title></info>

 <para>
-You can also show help for advanced options:
-% bali-phy --help=advanced | less
-% bali-phy --help=expert | less
-There is a shorter syntax for help topics:
-% bali-phy help advanced | less
-You can get help on models, distributions, functions, and command-line options:
+You can get extended help on each command line option:
+% bali-phy help iterations | less        // --iterations=&lt;num&gt; <emphasis>command line option</emphasis>
+% bali-phy help alphabet   | less        // --alphabet=&lt;a&gt; <emphasis>command line option</emphasis>
+You can also get help on models, distributions, functions, and command-line options:
 % bali-phy help tn93       | less        // Tamura-Nei (1993) <emphasis>model</emphasis>
 % bali-phy help normal     | less        // Normal <emphasis>distribution</emphasis>
 % bali-phy help quantile   | less        // quantile <emphasis>function</emphasis>
-% bali-phy help iterations | less        // --iterations=&lt;num&gt; <emphasis>command line option</emphasis>
+There are additional help topics you might want to explore:
+% bali-phy help topics     | less        // to see additional help topics
+% bali-phy help parameters | less        // setting parameters
+% bali-phy help Codons     | less        // Codons alphabets
 </para>

+  
 </section>

 <section ><info><title>Analysis 1: 5S rRNA -- free alignment versus fixed alignment</title></info>
@@ -489,8 +510,8 @@ This means that the branch lengths for partitions 1 and 3 are the same, instead
 </section>

 <section><info><title>Dataset preparation</title></info>
-<section><info><title>Splitting and Merging Alignments</title></info>
-<para>BAli-Phy generally wants you to split concatenated gene regions in order to analyze them.
+<section><info><title>Splitting and merging Alignments</title></info>
+<para>You might want to split concatenated gene regions:
 % cd ~/alignment_files/examples/ITS-many/
 % alignment-cat -c1-223 ITS-region.fasta > 1.fasta
 % alignment-cat -c224-379 ITS-region.fasta > 2.fasta
@@ -503,11 +524,17 @@ Later you might want to put them back together again:
 <section><info><title>Shrinking the data set</title></info>
 <para>
 You might want to reduce the number of taxa while attempting to preserve phylogenetic diversity:
-% alignment-thin --down-to=30 ITS-region.fasta > ITS-region-thinned.fasta
+% alignment-thin --cutoff=5 ITS-region.fasta -v --preserve=Csaxicola420 > ITS-region-thinned.fasta
+This removes sequences with 5 or fewer differences to the closest other sequence.
+<itemizedlist>
+  <listitem>The <userinput>-v</userinput> option shows which sequences are removed and the distance to their closest neighbor.</listitem>
+  <listitem>The <userinput>--preserve</userinput> option keeps specific sequences in the data set.</listitem>
+</itemizedlist>
+You can also specify that data sets should be shrunk to a specific number of sequences:
+% alignment-thin --down-to=30 ITS-region.fasta -v > ITS-region-thinned.fasta
 </para>
-<para>
-You can specify that certain sequences should not be removed:
-% alignment-thin --down-to=30 --keep=Csaxicola420 ITS-region.fasta > ITS-region-thinned.fasta
+<para>To see all options, run:
+% alignment-thin --help
 </para>
 </section>


--- a/doc/developer.md
+++ b/doc/developer.md
@@ -4,7 +4,9 @@

 ## Fork the repo

-1. Click the "Fork" button on [https://github.com/bredelings/BAli-Phy/](https://github.com/bredelings/BAli-Phy).  This will create a separate copy of the repo under your own account.
+This will create a separate copy of the repo under your own account.
+
+1. Click the "Fork" button on [https://github.com/bredelings/BAli-Phy/](https://github.com/bredelings/BAli-Phy).

 1. Use `git clone` to download your own version of the repo:
   ``` sh
@@ -15,7 +17,7 @@ The name `origin` in your local repo will then refer to your modified version of
 1. To refer to the official upstream version, create a new remote called `upstream`:
   ``` sh
   cd BAli-Phy/
-git remote add upstream git@github.com:bredelings/BAli-Phy.git
+   git remote add upstream https://github.com:bredelings/BAli-Phy.git
   git remote -v
   ```

@@ -49,17 +51,16 @@ These directories contain documentation and examples:
 [examples/models/](https://github.com/bredelings/BAli-Phy/blob/master/examples/models/)
 : Example files for running graphical models.

-## Contributions
-
-We are excited to see what you will contribute!
+## How to contribute

-The way to submit patches is:
+We are excited to see what you will contribute!  The way to submit changes is:

-1. First develop changes in your own repo.
+1. Fork the BAli-Phy repo to create your own repo.
+1. Develop changes on a branch in your own repo.
 1. Send a [pull request](https://help.github.com/articles/about-pull-requests/) through github.
-1. CI tests will run automatically on the on suggested  changes.
+1. Tests will run automatically on the on suggested changes.
 1. We will review the changes.
-1. If accepted, changes will be merged to the master branch.
+1. If accepted, changes will be merged to the master branch of the main repo.

 # Building bali-phy

@@ -106,10 +107,10 @@ ninja install
 Haskell functions are defined in the Haskell modules under [modules/](https://github.com/bredelings/BAli-Phy/blob/master/modules/).  For example, the function `min` is defined in `Prelude.hs` as follows:

 ``` Haskell
-min x y = if (x <= y) then x else y;
+min x y = if (x <= y) then x else y
 ```

-To add a Haskell function, you simply need to define a function in one of these modules.  However, be aware that the Haskell parser in bali-phy is not very advanced, and so you will need to specify `{`, `}`, and `;` in places where they are optional in standard Haskell.
+To add a Haskell function, you simply need to define a function in one of these modules.

 ## Adding a C++ function

@@ -120,13 +121,13 @@ To add a "builtin" C++ operation to bali-phy's Haskell code, you must add the C+
 A builtin is declared via the following syntax:

 ``` Haskell
-builtin haskell_name number_of_arguments "c++ name" "module name";
+builtin haskell_name number_of_arguments "c++ name" "module name"
 ```

 For example, the Haskell function `poisson_density` is declared with the following line from [modules/Distributions.hs](https://github.com/bredelings/BAli-Phy/blob/master/modules/Distributions.hs):

 ``` Haskell
-builtin poisson_density 2 "poisson_density" "Distribution";
+builtin poisson_density 2 "poisson_density" "Distribution"
 ```

 The first two arguments specify the Haskell name (`poisson_density`) and the number of arguments in Haskell (`2`).  The C++ function name is derived from the third argument (`poisson_density`) by adding `builtin_function_` in front.  So the C++ function will be called `builtin_function_poisson_density`.  The last argument specifies which loadable module contains the C++ function.  Since this function is in the module "Distribution", its source code goes in [src/builtins/Distribution.cc](https://github.com/bredelings/BAli-Phy/blob/master/src/builtins/Distribution.cc).
@@ -135,7 +136,7 @@ The first two arguments specify the Haskell name (`poisson_density`) and the num

 The C++ function for a builtin must be defined in one of the C++ files in the [src/builtins](https://github.com/bredelings/BAli-Phy/blob/master/src/builtins) directory, and the function name must begin with `builtin_function_`.  The function must also be declared `extern "C"` (to avoid name mangling).

-For example, the poisson density function is written in [src/builtins/Distirbution.cc](https://github.com/bredelings/BAli-Phy/blob/master/src/builtins/Distribution.cc) as follows:
+For example, the poisson density function is written in [src/builtins/Distribution.cc](https://github.com/bredelings/BAli-Phy/blob/master/src/builtins/Distribution.cc) as follows:

 ``` C++
 extern "C" closure builtin_function_poisson_density(OperationArgs& Args)
@@ -165,16 +166,16 @@ Distributions are defined in [modules/Distributions.hs](https://github.com/brede
 For a distribution, you need to add a function that constructs a ProbDensity object.

 ``` Haskell
-name parameters = ProbDensity (density parameters) (quantile parameters) (sample parameters) (range parameters);
+name parameters = ProbDensity (density parameters) (quantile parameters) (sample parameters) (range parameters)
 ```

 For example, the Normal distribution is defined as:
 ``` Haskell
-builtin normal_density 3 "normal_density" "Distribution";
-builtin normal_quantile 3 "normal_quantile" "Distribution";
-builtin builtin_sample_normal 2 "sample_normal" "Distribution";
-sample_normal m s = Random (IOAction2 builtin_sample_normal m s);
-normal m s = ProbDensity (normal_density m s) (normal_quantile m s) (sample_normal m s) realLine;
+builtin normal_density 3 "normal_density" "Distribution"
+builtin normal_quantile 3 "normal_quantile" "Distribution"
+builtin builtin_sample_normal 2 "sample_normal" "Distribution"
+sample_normal m s = Random (IOAction2 builtin_sample_normal m s)
+normal m s = ProbDensity (normal_density m s) (normal_quantile m s) (sample_normal m s) realLine
 ```

 ### Density
@@ -203,19 +204,20 @@ extern "C" closure builtin_function_sample_normal(OperationArgs& Args)
 ```
 Then use one of the following patterns, depending on how many arguments your sampling routine takes:
 ``` Haskell
-sample_dist arg1 = Random (IOAction1 builtin_sample_dist arg1);
-sample_dist arg1 arg2 = Random (IOAction2 builtin_sample_dist arg1 arg2);
-sample_dist arg1 arg2 arg3 = Random (IOAction3 builtin_sample_dist arg1 arg2 arg3);
+sample_dist arg1 = Random (IOAction1 builtin_sample_dist arg1)
+sample_dist arg1 arg2 = Random (IOAction2 builtin_sample_dist arg1 arg2)
+sample_dist arg1 arg2 arg3 = Random (IOAction3 builtin_sample_dist arg1 arg2 arg3)
 ```
 For example:
 ``` Haskell
-builtin builtin_sample_normal 2 "sample_normal" "Distribution";
-sample_normal m s = Random (IOAction2 builtin_sample_normal m s);
+builtin builtin_sample_normal 2 "sample_normal" "Distribution"
+sample_normal m s = Random (IOAction2 builtin_sample_normal m s)
 ```

 The `(dist_sample parameters)` function returns an object in the Random monad, where executing a distribution has the semantics of sampling from the distribution.  The sampling procedure can also call other actions in the Random monad. For example, here we sample from the distribution `(dist2 args)` and transform the result.
 ``` Haskell
-sample_dist args = do { x <- dist2 args; return (f x);}
+sample_dist args = do x <- dist2 args
+                      return (f x)
 ```

 ### Range
@@ -247,15 +249,11 @@ where `n` is the number of dimensions, and `sum` is the sum of the values (usual

 ## Using a function from the command line

-To make a Haskell function accessible from the command line, you must add a JSON file to the directory `functions/` that registers the Haskell function.
-
-For example, the file `functions/HKY.json` allows the user to specify (for example) `-S HKY[kappa=2]` as a substitution model.  It connects the command line phrase `HKY[kapp=2]` with the Haskell function `SModel.hky` defined in the file `modules/SModel.hs`.
-
-The JSON looks like this:
+To make a Haskell function accessible from the command line, you must add a JSON file to the directory `functions/` that registers the Haskell function.  For example, the file `functions/hky85.json` allows the user to specify (for example) `-S hky85[kappa=2]` as a substitution model.  The JSON looks like this:

 ``` json
 {
-    "name": "HKY",
+    "name": "hky85",
    "title": "The Hasegawa-Kishino-Yano (1985) nucleotide rate matrix",
    "result_type": "ExchangeModel[a]",
    "constraints": ["Nucleotides[a]"],
@@ -266,55 +264,64 @@ The JSON looks like this:
                "journal": {"name": "Journal of molecular evolution", "volume": "22", 
                "identifier": [{"type":"doi","id":"10.1007/BF02101694"}]
               },
-    "call": "SModel.hky[kappa,alphabet]",
+    "call": "SModel.Nucleotides.hky85[kappa,SModel.Frequency.frequencies_from_dict[a,pi],a]",
    "args": [
        {
            "arg_name": "kappa",
            "arg_type": "Double",
-            "default_value": "~logNormal[log[2],0.25]",
+            "default_value": "~log_normal[log[2],0.25]",
            "description": "Transition\/transversion ratio"
        },
        {
-            "arg_name": "alphabet",
+            "arg_name": "pi",
+            "arg_type": "List[Pair[String,Double]]",
+            "default_value": "~dirichlet_on[letters[@a],1]",
+            "description": "Letter frequencies"
+        },
+        {
+            "arg_name": "a",
            "arg_type": "a",
-            "default_value": "getAlphabet"
+            "default_value": "getAlphabet",
+            "description": "The alphabet"
        }
    ],
-    "description":"Technically, this is just the symmetric matrix from HKY"
+    "description":"The HKY85 model",
+    "extract": "all"
 }
 ```

 The fields are defined as follows:

 `name`
-: specifies how this function will be invoked on the command line.
+: The name of this function on the command line.

 `call`
-: specifies which Haskell function to call and the order of the arguments to pass.
+: The Haskell function to call, and the order of the arguments to pass.

 `result_type`
-: specifies the result type of the function.
+: The result type of the function.

 `args`
-: describes the list of named arguments
+: The the list of named arguments

 `args.arg_name`
-: gives the name of each argument
+: The name of each argument

 `args.arg_type`
-: gives the type of each argument
+: The type of each argument

 `args.default_value`
-: gives a value for the argument if not specified (optional).
+: A value for the argument if not specified (optional).

 `args.description`
-: gives a short phrase describing the argument (optional).
+: A short phrase describing the argument (optional).
+
+`title`
+: A title for the function (optional).

 `description`
-: gives a longer description of the function (optional).
+: A longer description of the function (optional).

-`title`
-: gives a title for the function (optional).

 ## Adding a new MCMC move


--- a/doc/docbook.css
+++ b/doc/docbook.css
@@ -59,15 +59,18 @@ pre {
 }

 pre.programlisting {
-    background-color: #F3F3E0;
+    border:solid;
+    background-color: #D0E3FF;
+    border-color:#BBB;
+    border-width:0.1em;
+    border-radius: 0.5em;

 //    border: solid green;
   margin: 0;
-	margin-left: 3em;
+   margin-left: 0.5em;

-	padding: 0.5em;
-	padding-left:1em;
-	width: calc(100% - 8em);
+   padding: 1em;
+   width: calc(100% - 4em);
 }

 pre.screen {

--- a/doc/man/alignment-cat.md
+++ b/doc/man/alignment-cat.md
@@ -4,7 +4,7 @@

 # NAME

-**alignment-cat** -- Concatenate several alignments (with the same sequence names) end-to-end.
+**alignment-cat** - Concatenate several alignments (with the same sequence names) end-to-end.

 # SYNOPSIS

@@ -57,22 +57,17 @@ Concatenate several alignments (with the same sequence names) end-to-end.

 # EXAMPLES:
 
-
-
-
 To select columns from an alignment:
-
+```
 % alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta
-
 % alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta
-
 % alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta
-
-
+```

 To concatenate two or more alignments:
-
+```
 % alignment-cat filename1.fasta filename2.fasta > all.fasta
+```

 # REPORTING BUGS:
 BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

--- a/doc/man/alignment-chop-internal.md
+++ b/doc/man/alignment-chop-internal.md
@@ -4,7 +4,7 @@

 # NAME

-**alignment-chop-internal** -- Remove ancestral sequences from an alignment.
+**alignment-chop-internal** - Remove ancestral sequences from an alignment.

 # SYNOPSIS


--- a/doc/man/alignment-compare.md
+++ b/doc/man/alignment-compare.md
@@ -4,7 +4,7 @@

 # NAME

-**alignment-compare** -- Compare two alignment distributions.
+**alignment-compare** - Compare two alignment distributions.

 # SYNOPSIS