Updated

CHANGELOG.md

@@ -0,0 +1,11 @@
+## SuperCRUNCH Version History
+
+- Version 1.1:
+  - Added multithreading option for MAFFT and Clustal-O in `Align.py`
+  - Added multithreading option for MAFFT in `Adjust_Direction.py`
+  - Added arg to specify output directory for `Concatenation.py`
+  - Corrected output column labeling in label key output files from `Relabel_Fasta.py`
+  - Added gappyout option for trimming with trimAl in `Trim_Alignments.py`
+  - Output sequences failing similarity searches to own file in `Cluster_Blast_Extract.py` and `Reference_Blast_Extract.py`
+  - Updated documentation on wiki pages
+

README.md

@@ -17,12 +17,12 @@ A full overview of **SuperCRUNCH** is described in the following pre-print artic
 
 ## Version
 
-The current release of **SuperCRUNCH** is v1.0.
+The current release of **SuperCRUNCH** is [v1.1](https://github.com/dportik/SuperCRUNCH/releases). For version history please see the [change log file](https://github.com/dportik/SuperCRUNCH/tree/master/CHANGELOG.md).
 
 
 ## Installation
 
-**SuperCRUNCH** consists of a set of modules written in Python (2.7) that function as stand-alone command-line scripts. These modules are available in the [supercrunch-scripts](https://github.com/dportik/SuperCRUNCH/tree/master/supercrunch-scripts) folder. They can be downloaded and executed independently without the need to install SuperCRUNCH as a Python package or library, making them easy to use and edit. The scripts function independently, and do not require being contained or used in the same directory. There are several external dependencies that should be installed prior to use of SuperCRUNCH, including:
+**SuperCRUNCH** consists of a set of modules written in Python (2.7) that function as stand-alone command-line scripts. These modules are available in the [supercrunch-scripts](https://github.com/dportik/SuperCRUNCH/tree/master/supercrunch-scripts) folder. They can be downloaded and executed independently without the need to install SuperCRUNCH as a Python package or library, making them easy to use and edit. The scripts function independently, and do not require being contained or used in the same directory. There are several external dependencies that should be installed prior to use of SuperCRUNCH if you plan to use all the available modules, including:
 
 + [Biopython](https://biopython.org/)
 + [NCBI-BLAST+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
@@ -34,6 +34,8 @@ The current release of **SuperCRUNCH** is v1.0.
 + [trimAl](http://trimal.cgenomics.org/)
 
 Helpful installation instructions for these dependencies can be found on the [wiki installation page](https://github.com/dportik/SuperCRUNCH/wiki/Installation-Instructions).
+Please note that some modules do not require any dependencies. If you plan to use only a subset of modules you can quickly check which modules require dependencies [here](https://github.com/dportik/SuperCRUNCH/wiki/Installation-Instructions). 
+
 SuperCRUNCH scripts can be run using Mac OSX (10.10+) and Linux, and can also work with Windows if using Cygwin.