Update README.md

README.md

@@ -31,11 +31,11 @@ A **gene call** is an optimal set of exons predicted based on similarity to a sp
 ## Running MetaEuk 
 ### Main Modules:
 
+      easy-predict      	Predict proteins from contigs (fasta/db) based on similarities to targets (fasta/db) and return a fasta
       predictexons      	Call optimal exon sets based on protein similarity
       reduceredundancy  	Cluster metaeuk calls which share an exon and select representative
       unitesetstofasta  	Create a fasta output from optimal exon sets
       groupstoacc     	Create a TSV output from representative to calls
-      easy-predict      	Predict proteins from contigs (fasta/db) based on similarities to targets (fasta/db) and return a fasta
 
 
 ### Important parameters: 
@@ -47,6 +47,13 @@ A **gene call** is an optimal set of exons predicted based on similarity to a sp
      --slice-search      if refernceDB is a profile database, should be added
      
 
+### easy-predict workflow:
+
+This workflow combines the following MetaEuk modules into a single step: predictexons, reduceredundancy and unitesetstofasta (each of which is detailed below). Its input are contigs (either as a Fasta file or a previously created database) and targets (either as a Fasta file of protein sequences or a previously created database of proteins or protein profiles). It will run the modules and output the predictions in Fasta foramt.
+
+    metaeuk easy-predict contigsFasta/contigsDB proteinsFasta/referenceDB predsResultProteins.fas tempFolder
+
+
 ### Calling optimal exons sets:
 
 This module will extract all putative protein fragments from each contig and strand, query them against the reference targets and use dynamic programming to retain for each **T** the optimal compatible exon set from each **C** & **S** (thus creating **TCS** calls).
@@ -102,12 +109,6 @@ can help mapping from each representative prediction after the redundancy reduct
     metaeuk groupstoacc contigsDB referenceDB predGroupsDB predGroups.tsv
 
 
-### easy-predict workflow:
-
-This workflow combines the following MetaEuk modules into a single step: predictexons, reduceredundancy and unitesetstofasta. Its input are contigs (either as a Fasta file or a previously created database) and targets (either as a Fasta file of protein sequences or a previously created database of proteins or protein profiles). It will run the modules and output the predictions in Fasta foramt.
-
-    metaeuk easy-predict contigsFasta/contigsDB proteinsFasta/referenceDB predsResultProteins.fas tempFolder
-
 
 ## Compile from source
 Compiling MetaEuk from source has the advantage that it will be optimized to the specific system, which should improve its performance. To compile MetaEuk `git`, `g++` (4.6 or higher) and `cmake` (3.0 or higher) are required. Afterwards, the MetaEuk binary will be located in the `build/bin` directory.