From d129c3f5abf63abdaa5a81c5aaa10fb32f5633f8 Mon Sep 17 00:00:00 2001
From: Frederic Lemoine <fredericlemoine@users.noreply.github.com>
Date: Thu, 30 Jan 2020 19:26:43 +0100
Subject: [PATCH] Documentation nni

---
 docs/api/nni.md      | 52 ++++++++++++++++++++++++++++++++++++++++++
 docs/commands/nni.md | 54 ++++++++++++++++++++++++++++++++++++++++++++
 docs/index.md        |  1 +
 3 files changed, 107 insertions(+)
 create mode 100644 docs/api/nni.md
 create mode 100644 docs/commands/nni.md

diff --git a/docs/api/nni.md b/docs/api/nni.md
new file mode 100644
index 0000000..bc866b4
--- /dev/null
+++ b/docs/api/nni.md
@@ -0,0 +1,52 @@
+# Gotree: toolkit and api for phylogenetic tree manipulation
+
+## API
+
+### nni
+
+Merging two trees
+
+```go
+package main
+
+import (
+	"fmt"
+	"os"
+
+	"github.com/evolbioinfo/gotree/io/newick"
+	"github.com/evolbioinfo/gotree/tree"
+)
+
+func main() {
+	var t *tree.Tree
+	var f *os.File
+	var err error
+
+	if f, err = os.Open("t1.nw"); err != nil {
+		panic(err)
+	}
+	defer f.Close()
+	if t, err = newick.NewParser(f).Parse(); err != nil {
+		panic(err)
+	}
+
+	r := &tree.NNIRearranger{}
+
+	r.Rearrange(t, func(re tree.Rearrangement) bool {
+		if err = re.Apply(); err != nil {
+			return false
+		}
+		if err = t.CheckTreePostOrder(); err != nil {
+			return false
+		}
+		fmt.Println(t.Newick())
+		if err = re.Undo(); err != nil {
+			return false
+		}
+		if err = t.CheckTreePostOrder(); err != nil {
+			return false
+		}
+		return true
+	})
+}
+```
diff --git a/docs/commands/nni.md b/docs/commands/nni.md
new file mode 100644
index 0000000..66465c2
--- /dev/null
+++ b/docs/commands/nni.md
@@ -0,0 +1,54 @@
+# Gotree: toolkit and api for phylogenetic tree manipulation
+
+## Commands
+
+### nni
+This command generates all NNI neighbors from a given tree.
+
+#### Usage
+
+```
+Usage:
+  gotree nni [flags]
+
+Flags:
+  -h, --help            help for nni
+  -i, --input string    Input Tree (default "stdin")
+  -o, --output string   NNI output tree file (default "stdout")
+
+Global Flags:
+      --format string   Input tree format (newick, nexus, or phyloxml) (default "newick")
+```
+
+#### Example
+
+* Generates NNI neighbors
+
+```
+echo "(n1_1,n1_2,(n2_1,n2_2)n2)n1;" | gotree nni
+```
+
+It should give the following trees:
+```
+(n1_1,n2_2,(n2_1,n1_2)n2)n1;
+(n1_1,n2_1,(n1_2,n2_2)n2)n1;
+```
+
+
+Tree:
+```
+n1_1 ---------------+                +--------------- n2_1
+                    |----------------|                            
+n1_2 ---------------+                +--------------- n2_2
+```
+
+NNIs:
+```
+n1_1 ---------------+                +--------------- n2_1
+                    |----------------|                            
+n2_2 ---------------+                +--------------- n1_2
+
+n1_1 ---------------+                +--------------- n1_2
+                    |----------------|                            
+n2_1 ---------------+                +--------------- n2_2
+```
diff --git a/docs/index.md b/docs/index.md
index 656ebec..6603c8a 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -80,6 +80,7 @@ Command                                                            | Subcommand
 --                                                                 | yuletree          | Randomly generates Yule-Harding trees
 [matrix](commands/matrix.md) ([api](api/matrix.md))                |                   | Prints distance matrix associated to the input tree
 [merge](commands/merge.md) ([api](api/merge.md))                   |                   | Merges two rooted trees
+[nni](commands/nni.md) ([api](api/nni.md))                   |                   | Generates all NNI neighbors from a given tree
 [prune](commands/prune.md) ([api](api/prune.md))                   |                   | Removes tips of input trees
 [reformat](commands/reformat.md) ([api](api/reformat.md))          |                   | Reformats input file
 --                                                                 | newick            | Reformats input file (nexus, newick, phyloxml) into newick