diff --git a/.gitignore b/.gitignore
index eacd853..0d5db07 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+.DS_Store
 .idea
 target
 *.iml
diff --git a/README.md b/README.md
index 56d0129..f995d12 100644
--- a/README.md
+++ b/README.md
@@ -36,7 +36,7 @@ managers within your Galaxy instance. These can be found at:
 | snippy                             | `4.4.5`         | `iuc`                          | 10 (2020-01-30)   | [snippy-10:3fe8ef358d66](https://toolshed.g2.bx.psu.edu/view/iuc/snippy/3fe8ef358d66)            |
 | gubbins                            | `2.2.1`         | `iuc`                          |  0 (2017-06-23)   | [gubbins-0:637ec5d5368c](https://toolshed.g2.bx.psu.edu/view/iuc/gubbins/637ec5d5368c)           |
 | snp_sites                          | `2.5.1`         | `iuc`                          |  1 (2019-11-02)   | [snp_sites-1:5804f786060d](https://toolshed.g2.bx.psu.edu/view/iuc/snp_sites/5804f786060d)       |
-| iqtree                             | `1.5.5`         | `iuc`                          |  3 (2020-01-29)   | [iqtree-3:973a28be3b7f](https://toolshed.g2.bx.psu.edu/view/iuc/iqtee/973a28be3b7f)              |
+| iqtree                             | `1.5.5.3`       | `iuc`                          |  4 (2020-04-03)   | [iqtree-4:f97743d52b87](https://toolshed.g2.bx.psu.edu/view/iuc/iqtee/f97743d52b87)              |
 
 **NOTE**: There is currently an unresolved issue in snippy involving a problem resolving the correct version number for samtools. This issue arises when snippy is installed from bioconda, as is normally the case when installing to galaxy. The issue can be resolved by:
 
@@ -56,7 +56,9 @@ Please download the provided `irida-plugin-snippy-phylogenomics-[version].jar` f
 The plugin should now show up in the **Analyses > Pipelines** section of IRIDA.
 
 ![plugin-pipeline.png][]
-![pipeline-parameters.png][]
+![pipeline-parameters-1.png][]
+![pipeline-parameters-2.png][]
+
 
 ## Analysis Results
 
@@ -145,6 +147,8 @@ The following dependencies are required in order to make use of this plugin.
 [plugin-results-3.png]: doc/images/plugin-results-3.png
 [plugin-pipeline.png]: doc/images/plugin-pipeline.png
 [plugin-metadata.png]: doc/images/plugin-metadata.png
-[pipeline-parameters.png]: doc/images/pipeline-parameters.png
+[pipeline-parameters-1.png]: doc/images/pipeline-parameters-1.png
+[pipeline-parameters-2.png]: doc/images/pipeline-parameters-2.png
+
 [example-plugin-save-results.png]: doc/images/example-plugin-save-results.png
 [galaxy-workflow-diagram.png]: doc/images/galaxy-workflow-diagram.png
diff --git a/doc/images/pipeline-parameters-1.png b/doc/images/pipeline-parameters-1.png
new file mode 100644
index 0000000..d820edd
Binary files /dev/null and b/doc/images/pipeline-parameters-1.png differ
diff --git a/doc/images/pipeline-parameters-2.png b/doc/images/pipeline-parameters-2.png
new file mode 100644
index 0000000..b9a96ce
Binary files /dev/null and b/doc/images/pipeline-parameters-2.png differ
diff --git a/doc/images/pipeline-parameters.png b/doc/images/pipeline-parameters.png
deleted file mode 100644
index 1dde7ec..0000000
Binary files a/doc/images/pipeline-parameters.png and /dev/null differ