From 202ff17a11e7d17a4955bc894f7795ee5b789133 Mon Sep 17 00:00:00 2001
From: Ward9250 <axolotlfan9250@gmail.com>
Date: Mon, 23 May 2016 22:50:23 +0100
Subject: [PATCH] Begun docs for Phylo.

---
 docs/mkdocs.yml       |  1 +
 docs/src/index.md     |  1 +
 docs/src/man/phylo.md | 49 +++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 51 insertions(+)
 create mode 100644 docs/src/man/phylo.md

diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index 0e92f997c..9093cead5 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -45,6 +45,7 @@ pages:
   - IO API: man/reading.md
   - Biological Sequences: man/seq.md
   - Alignments: man/alignments.md
+  - Phylogenetics: man/phylo.md
   - Intervals: man/intervals.md
   - Structure: man/structure.md
   - Tools: man/tools.md
diff --git a/docs/src/index.md b/docs/src/index.md
index d33d9b2b5..9df1b17eb 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -5,6 +5,7 @@ Pages = [
     "man/install.md",
     "man/seq.md",
     "man/alignments.md",
+    "man/phylo.md",
     "man/intervals.md",
     "man/structure.md",
     "man/tools.md"
diff --git a/docs/src/man/phylo.md b/docs/src/man/phylo.md
new file mode 100644
index 000000000..188fa2209
--- /dev/null
+++ b/docs/src/man/phylo.md
@@ -0,0 +1,49 @@
+# Bio.Phylo: Phylogenetic trees and models of ancestry
+
+```@meta
+CurrentModule = Bio.Phylo
+DocTestSetup = quote
+    using Bio.Phylo
+end
+```
+
+The `Bio.Phylo` module provides data types and methods for working with
+phylogenetic trees and other similar structures that model evolutionary history
+and relatedness between taxa.
+
+## Types
+
+### Phylogenies
+
+The phylogeny datatype represents phylogenetic trees in BioJulia.
+
+The internal structure and representation of the Phylogeny type uses a DiGraph.
+DiGraph is a type representing a directed graph and is implemented in the
+LightGraphs.jl package.
+When a phylogenetic tree is created, the DiGraph is initiated with enough vertices
+to be able to represent a fully bifurcating phylogeny, no more and no less.
+The vertices of the DiGraph are reserved for different specific purposes.
+
+Vertex ranges:
+* 1:tree.ntaxa => leaf vertices
+* tree.ntaxa + 1 => root vertex
+* tree.ntaxa + 1:<#nodes> => clade vertices
+
+As it is common to annotate phylogenies with data, the type is parametric with
+two parameters C, and B. Parameter C represents a datatype that annotates clades
+of the phylogeny, and parameter B represents a datatype that annotates branches
+of the phylogeny.
+
+Phylogenies can be created with the provided constructors for example,
+constructing a phylogeny from just an array of Taxa names creates a basic and
+fully unresolved star phylogeny, which can annotate clades and branches with
+`Float64` values, which enables you to annotate branch lengths to branches and
+confidence values to clades.
+
+```jlcon
+julia> tree = Phylogeny([:Human, :Chimp, :Dog, :Fish])
+Bio.Phylo.Phylogeny{Float64,Float64}({7, 4} directed graph,Bio.Indexers.Indexer{Int64}(Dict(:Fish=>4,:Dog=>3,:Chimp=>2,:Root=>5,:Human=>1),[:Human,:Chimp,:Dog,:Fish,:Root]),Float64[],Dict{Pair{Int64,Int64},Float64}(),4,false,true)
+
+julia> tree = Phylogeny(["Human", "Chimp", "Dog", "Fish"])
+Bio.Phylo.Phylogeny{Float64,Float64}({7, 4} directed graph,Bio.Indexers.Indexer{Int64}(Dict(:Fish=>4,:Dog=>3,:Chimp=>2,:Root=>5,:Human=>1),[:Human,:Chimp,:Dog,:Fish,:Root]),Float64[],Dict{Pair{Int64,Int64},Float64}(),4,false,true)
+```