Update README.txt

README.txt

@@ -1,6 +1,6 @@
 # GenAPI
 
-GenAPI is a program for gene presence absence table generation for series of closely related bacterial genomes from annotated GFF files. For genome annotation [prokka](https://github.com/tseemann/prokka) software could be used.
+GenAPI is a program for gene presence absence table generation for series of closely related bacterial genomes from annotated GFF files. For genome annotation prokka software could be used.
 
 ### Purpose
 
@@ -23,33 +23,33 @@ RAxML >=8.2.11
 ### Installation
 
 Clone the repository:
-```
+
 git clone https://github.com/MigleSur/GenAPI.git
-```
+
 
 Add the following line to your .bashrc
 (if the GenAPI is located in a different directory than /bin/bash, use the path to that directory):
-```
+
 export PATH=$PATH:/usr/bin/GenAPI/bin
-```
+
 
 Reload the .bashrc file by running:
-```
+
 source ~/.bashrc
-```
+
 
 To run the program move to the folder where the output files should be produced and run:
-```
+
 genapi [options] [-n <analysis name>]
-```
+
 
 ### Input
 
 Annotated contig/scaffold/genome GFF files of the chosen samples have to be placed in the directory from which the program is being run. GenAPI uses unique IDs from the GFF file as annotations, so it would be easy to trace back the gene of interest. 
 
 ### Usage
 
-```
+
 Usage: genapi [options] [--name <analysis name>]
 
         -n, --name      Chosen analysis name.
@@ -80,7 +80,8 @@ Usage: genapi [options] [--name <analysis name>]
 
         -v, --version   Print the tool version.
         -h, --help      Print this message.
-```
+
+
 First minimum alignment length threshold and first minimum identity threshold are used as a pair. The same goes for the second pair. It is not advised to change those arguments unless there is a strong reason for doing that.
 
 The minimum length requirement for the gene to be included in the gene presence-absence matrix is 150 bp, it can be changed but not recommended unless it was made sure that lower threshold is required.