Fix README

README.md

@@ -19,8 +19,7 @@ For a list of priority categories and ranks for all virus species in the paper,
 ## Requirements
 
 - Install the [conda package manager](https://conda.io/)
-- Create the base environment
-This installs everything required for prediction of new viruses
+- Create the base environment (this installs everything required for prediction of new viruses)
 ```
 conda env create -f base_environment.yml
 ```
@@ -44,9 +43,9 @@ The [BLAST+ suite of applications](https://www.ncbi.nlm.nih.gov/books/NBK279670/
 Ranks for novel viruses can be generated by specifying the input sequence format, paths to genome and metadata files, and a name for output files, e.g:
 ```
 Rscript Scripts/PredictNovel.R fasta \
-                       InternalData/example_files/genomes.fasta \
-                       InternalData/example_files/metadata.csv \
-                       example_1
+                               InternalData/example_files/genomes.fasta \
+                               InternalData/example_files/metadata.csv \
+                               example_1
 ```
 
 For detailed instructions and further options, see
@@ -113,12 +112,12 @@ make clean all
 ```
 └─zoonotic_rank/
    ├─Makefile ................................. Record of workflow and dependencies between files
-   ├─options.config ........................... Runtime options (speciefies number of parrallel
+   ├─options.config ........................... Runtime options (specifies number of parrallel
    │                                            threads allowed and the random seed)
    ├─base_environment.yml ..................... Record of software and R libraries required for 
    │                                            prediction
    ├─dev_environment.yml ...................... Record of additional software required to train and
-   │                                            evaulate models
+   │                                            evaluate models
    ├─InternalData/ ............................ All data unique to this project
    │   ├─example_files/ ....................... Example input files for predicting novel viruses
    │   ├─Shaw2017_raw/ ........................ Raw ISG data from Shaw et al. 2017