diff --git a/docs/source/interfaces/Frequency_domain_analysis.rst b/docs/source/interfaces/Frequency_domain_analysis.rst
index 80121321146fa4d05f0671774768fc8f24e17846..749bcbf2d33b24faac74007fc4db262eb3b5cb74 100644
--- a/docs/source/interfaces/Frequency_domain_analysis.rst
+++ b/docs/source/interfaces/Frequency_domain_analysis.rst
@@ -18,6 +18,9 @@ accessed from the main menu of MantidPlot, in *Interfaces → Muon → Frequency
datasets, please visit `Muon - Downloads <http://www.isis.stfc.ac.uk/groups/muons/downloads/downloads4612.html>`_.
This interface is currently still in development. The data needs to be loaded and prepared using :ref:`Muon_Analysis-ref`.
+When Frequency Domain Analysis is opened it will import the groups/pairs from the current run in Muon Analysis,
+** if no data has been loaded into Muon Analysis then Frequency Domain Analysis will not open**.
+
Analysis of the frequency spectrum can be achieved by clicking the fit function icon.
As the interfaces is developed the features from Muon Analysis will be replicated.
@@ -33,12 +36,16 @@ Default: Fast Fourier Transforms
.. image:: ../images/FDAG_FFT.png
:align: center
- :height: 400px
+ :height: 500px
In this mode the interface displays two tables, FFT and Advanced options. The FFT table contains
all of the information required to produce a forward FFT. The Advanced Options table contains the information
for adding padding and apodization functions to the data.
+Selecting the workspace to be ``PhaseQuad`` will cause the :ref:`PhaseQuad <algm-PhaseQuad>` algortihm to be called first. If no phase table is available then
+the interface will generate one and output the result as ``PhaseTable``. It is possible to select the direction of the axis when generating the table and it is
+possoble to use a pre-existing ``PhaseTable``. **Note that the PhaseQuad option requires the data archieve to be in the search directory.
+
The Calculate button will execute the :ref:`Padding and Apodization <algm-PaddingAndApodization>` and then :ref:`FFT <algm-FFT>` algortihms. The output workspace will be added to
``FFTMuon``.
@@ -55,7 +62,7 @@ For large calculations this interface can be slow, therefore the Calculate butto
.. image:: ../images/FDAG_MaxEnt.png
:align: center
- :height: 400px
+ :height: 500px
Feedback & Comments
-------------------
diff --git a/docs/source/interfaces/Muon Analysis Unscripted Testing Guide.rst b/docs/source/interfaces/Muon Analysis Unscripted Testing Guide.rst
index 5424acbd50768eeabe4514397be6d9c6d7a613b9..1b586ac87ad75c830349f76c46a3f47bdd47faca 100644
--- a/docs/source/interfaces/Muon Analysis Unscripted Testing Guide.rst
+++ b/docs/source/interfaces/Muon Analysis Unscripted Testing Guide.rst
@@ -15,7 +15,7 @@ Testing here mostly focuses on the changes for Mantid 3.11, but includes other f
The tests follow real use cases provided by scientists and are intended to exercise all the interface's functionality.
As changes are made to the interface and features added, anything for which it is not possible to write an automated test should have a manual test added to this list.
-.. note:: The tests here are grouped into five sections. The test groups should be run in order and, within each test group, the individual tests should also be run in order. This is because, to avoid duplication, some tests rely on previous tests having been run first.
+.. note:: The tests here are grouped into four sections. The test groups should be run in order and, within each test group, the individual tests should also be run in order. This is because, to avoid duplication, some tests rely on previous tests having been run first.
Common setup
^^^^^^^^^^^^
diff --git a/docs/source/interfaces/Muon Analysis.rst b/docs/source/interfaces/Muon Analysis.rst
index 746c938f2b343ff2a2510c3e0dff2b8db1b57e36..7667d1af375c2722fe391c11d8d3b663e37f49af 100644
--- a/docs/source/interfaces/Muon Analysis.rst
+++ b/docs/source/interfaces/Muon Analysis.rst
@@ -14,7 +14,10 @@ Interface Overview
This interface is used to analyse the data collected on Muon instruments. The interface can be
accessed from the main menu of MantidPlot, in *Interfaces → Muon → Muon Analysis*. For sample
-datasets, please visit `Muon - Downloads <http://www.isis.stfc.ac.uk/groups/muons/downloads/downloads4612.html>`_.
+datasets, please visit `Muon - Downloads <http://www.isis.stfc.ac.uk/groups/muons/downloads/downloads4612.html>`_.#
+
+If the :ref:`Frequency_Domain_Analysis-ref` interfaces is opened it will import all of the data available for the current run in Muon Analysis.
+This will include any custom groupings/pairs.
Home
----
diff --git a/docs/source/interfaces/MuonAnalysis_test_guides/Muon_Analysis_test_group_4_FDAG.rst b/docs/source/interfaces/MuonAnalysis_test_guides/Muon_Analysis_test_group_4_FDAG.rst
index e137b5631617f3b68be2a194b3281ec5d06edb5e..d1013f37cb8a54b763bc9d722c5afa02264feb31 100644
--- a/docs/source/interfaces/MuonAnalysis_test_guides/Muon_Analysis_test_group_4_FDAG.rst
+++ b/docs/source/interfaces/MuonAnalysis_test_guides/Muon_Analysis_test_group_4_FDAG.rst
@@ -10,7 +10,7 @@ Introduction
^^^^^^^^^^^^
These are unscripted tests for the :program:`Frequency Domain Analysis` interface.
-In this case, runs from test group 2 are used, so those tests need to be run before these ones.
+Load "MUSR00062260" into Muon analysis and plot each of the available groups **before** opening Frequency Domain Analysis.
The master testing guide is located at :ref:`Muon_Analysis_TestGuide-ref`.
@@ -22,7 +22,7 @@ Ensure that you have first run all the tests in group 2, then open the Frequency
Test 1: Basic FFT
-----------------
- Set the workspace to "MUSR00062260;Group;bkwd;Asym;#1"
-- Click the calculate FFT button and a workspace should appear "FFTMuon"
+- Click the calculate FFT button and a workspace should appear in the "MUSR00062260" group
- Then plot spectrum 2 (there should be a total of 3 spectrums)
- You will see a few sharp peaks.
- Untick the Imaginary Data and the a row should disappear
@@ -42,7 +42,21 @@ Test 2: Advanced FFT
- Click the Calculate FFT Button
- The peak should not be very clear
-Test 3: MaxEnt
+Test 3: PhaseQuad
+-----------------
+- Change the workspace to "PhaseQuad"
+- You should not be able to select the workspace for the imaginary part, but it is possible to turn the imaginary component on and off.
+- An extra row will appear labeled "axis"
+- Click the Calculate FFT button
+- A new table workspace will appear (PhaseTable) and the output added to the grouped worksapce
+- Open PhaseTable and with it open change the axis in the GUI and make sure that generate new phase table is unticked
+- Click the Calculate FFT button
+- PhaseTable should not have changed
+- Make sure that generate new phase table is ticked
+- Click the Calculate FFT button
+- PhaseTable should change
+
+Test 4: MaxEnt
--------------
- Change the drop-down menu at the top of the interface to "MaxEnt"
- The interface should look different