README updated

README.md

@@ -42,7 +42,6 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
 
   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:
@@ -53,10 +52,17 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
                               (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
 
+  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)