update to version 1.2

Author: gvignolle

README.md

@@ -1,11 +1,12 @@
+
 FunOrder
 =========
 
 The Functional Order (FunOrder) tool - Identification of essential biosynthetic genes through computational molecular co-evolution – searches for co-evolutionary linked genes in a set of inputted genes. The functionality and applicability was tested with biosynthetic gene clusters (BGCs). The resulting information can be used to choose which genes of a gene cluster are most likely the core genes necessary for the biosynthesis of a secondary metabolite. The flexibility and adaptability of the core program allows the integration of any protein database and can thus be adapted for different phyla and research objectives. FunOrder might be used for the analysis of co-evolution on a whole proteome, enabling the genome wide detection of evolutionary linked genes, in the future. 
 
 The Functional Order (FunOrder) tool - Identification of essential biosynthetic genes through computational molecular co-evolution. FunOrder is copyright 2020 Gabriel A. Vignolle, Denise Schaffer, Robert L. Mach, Astrid R. Mach-Aigner and Christian Derntl, and is released under the MIT License. If you find FunOrder useful to your work, please cite:
 
-https://zenodo.org/record/4778487 for the code or 
+https://zenodo.org/record/4778487 for the code or
 
 **The Functional Order (FunOrder) tool - Identification of essential biosynthetic genes through computational molecular co-evolution** Gabriel A Vignolle, Denise Schaffer, Robert L Mach, Astrid R Mach-Aigner, Christian Derntl. **bioRxiv** 2021.01.29.428829; doi: https://doi.org/10.1101/2021.01.29.428829
 
@@ -19,14 +20,13 @@ The three distance matrices are first visualized as heatmaps with a dendrogram c
 Dependencies
 ------------
 
-Third party programs (include Emboss, RAxML and ClustalW in your $PATH)
+Third party programs
 
 * [Python 2](https://www.anaconda.com)
 * [Perl](https://www.perl.org/get.html)
 * [R](https://www.r-project.org/)
 * [Emboss](http://emboss.sourceforge.net/download/)
 * [RAxML](https://github.com/stamatak/standard-RAxML)
-* [ClustalW](http://www.clustal.org/clustal2/)
 
 Perl packages:
 
@@ -43,14 +43,15 @@ R packages:
 * gplots
 * car
 * mdatools
+* randtests
 
 Installation
 ------------
 
 These instructions should work on [Debian](https://www.debian.org)-based linux distributions such as [Ubuntu](https://www.ubuntu.com).
 
 First we install the EMBOSS package according to the instructions.
-Then we install RAxML and ClustalW according to the instructions and place the executables in your $PATH.
+Then we install RAxML according to the instructions.
 After R, Perl and Python is installed, install the ete2 package.
 
 ```
@@ -67,7 +68,7 @@ install.packages('car') # at the R prompt
 install.packages('mdatools') # at the R prompt
 ```
 
-Now download the newest version of FunOrder **funorder_vxx.tar.xz** and unpack the archive.
+Now download FunOrder **funorder_v1.tar.xz** and unpack the archive.
 
 ```
 tar -xf funorder_v1.tar.xz
@@ -89,6 +90,7 @@ Alternativeley you can call the FunOrder/pipeline directory directly.
 
 
 
+
 ### 1) using FunOrder in default mode with Genbank files
 ------------
 
@@ -124,6 +126,7 @@ evol_distance.matrix         | matrix of the evolutionary [speciation] distance
 
 
 
+
 ### 2) using FunOrder in default mode with fasta files
 ------------
 
@@ -159,6 +162,7 @@ evol_distance.matrix         | matrix of the evolutionary [speciation] distance
 
 
 
+
 ### 3) using FunOrder in server mode with gbk files
 ------------
 
@@ -205,9 +209,8 @@ then from within the antiSMASH output-folder run following command:
 ```
 for file in *cluster*.gbk; do echo $file; sh ~/path/to/directory/funorder_v1/funorder_server.sh [Thread number] $file [absolute path to "funorder_output" directory] [database] ; done
 ```
-This will perform a FunOrder analysis for each cluster predicted by antiSMASH.
-
 
+This will perform a FunOrder analysis for each cluster predicted by antiSMASH.
 
 ### 4) using FunOrder in server mode with fasta files
 ------------
@@ -241,4 +244,3 @@ Rplot.pdf                    | PDF file with the Analyze.R output as described i
 strict_distance.matrix       | matrix of the strict distance
 evol_distance.matrix         | matrix of the evolutionary [speciation] distance
 
-

funorder_v1.1.tar.xz

@@ -0,0 +1,3 @@
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+size 678064748