README updated

README.md

@@ -40,30 +40,36 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
 ```
   USAGE: metaclade2 -i <input_fasta> -N <name> [options]
 
-  MANDATORY OPTIONS:    
+  MANDATORY OPTIONS:
     -i, --input <path>  Input file of AA sequences in FASTA format
-                        (protein sequences or predicted CDS)
     -N, --name <str>    Dataset/job name
 
-  MetaCLADE OPTIONS:              
-    -a, --arch                    Use DAMA to properly compute domain architectures
-                                  (useful only for long protein sequences)
-    -d, --domain-list <str>       Comma-spearated list of Pfam accession numbers of
-                                  the domains to be considered in the analysis
-                                  (e.g., "PF00875,PF03441")
-    -D, --domain-file <path>      File that contains the Pfam accession numbers
-                                  of the domains to be considered (one per line)
-    -e, --evalue-cutoff <float>   E-value cutoff
-    -E, --evalue-cutconf <float>  Confidence threshold used by DAMA to add new domains into the architecture.
-    -W, --work-dir <path>         Working directory, where jobs and results are saved
-
-  OTHER OPTIONS:         
+  MetaCLADE OPTIONS:
+    -a, --arch                Use DAMA to properly compute domain architectures
+                              (useful only for long protein sequences)
+    -d, --domain-list <str>   Comma-spearated list of Pfam accession numbers of
+                              the domains to be considered in the analysis
+                              (e.g., "PF00875,PF03441")
+    -D, --domain-file <path>  File that contains the Pfam accession numbers
+                              of the domains to be considered (one per line)
+    -W, --work-dir <path>     Working directory, where jobs and results are saved
+
+  DAMA OPTIONS:
+    -e, --evalue-cutoff <float>   E-value cutoff (default:1e-3)
+    -E, --evalue-cutconf <float>  Confidence threshold to add new domains in the architecture.
+                                  (default:1e-10)
+    --overlappingAA <num>         number (>=0) of amino acids allowed in the domain overlapping.
+                                  (default:30)
+    --overlappingMaxDomain <num>  domain overlapping is allowed for at most <num>% of the match
+                                  (default:50)
+
+  OTHER OPTIONS:
     -j, --jobs <num>     Number of jobs to be created (default:16)
     -t, --threads <num>  Number of threads for each job (default:1)
     -h, --help           Print this help message
     -V, --version        Print version
 
-  SGE OPTIONS:               
+  SGE OPTIONS:
     --sge                    Run MetaCLADE jobs on a SGE HPC environment
     --pe <name>              Parallel environment to use (mandatory)
     --queue <name>           Name of a specific queue where jobs are submitted