Initial commit

README.md

@@ -8,28 +8,28 @@ To use correctly the model you need to run this command line :
 
 ## Initial models (stringent)
 
-For T2SS Tad T4aP T4bP MSH ComM
+For T2SS Tad T4aP ComM
 
 ```
-macsyfinder -w 4 -d DEF_TFF-SF_final/ -p profiles_TFF-SF_final/ -o macsyfinder_T2SS-Tad-T4P-T4bP-MSH-ComM --db-type ordered_replicon --sequence-db sequence.fasta T2SS Tad T4P T4bP MSH ComM
+macsyfinder -w 4 -d DEF_TFF-SF_stringent/ -p profiles_TFF-SF_stringent/ -o macsyfinder_T2SS-Tad-T4P-T4bP-MSH-ComM --db-type ordered_replicon --sequence-db sequence.fasta T2SS Tad T4P ComM
 ```
 
 For Archaeal-T4P
 
 ```
-macsyfinder -w 4 -d DEF_TFF-SF_final/ -p profiles_TFF-SF_final/ -o macsyfinder_Archaeal-T4P --db-type ordered_replicon --sequence-db sequence.fasta Archaeal-T4P
+macsyfinder -w 4 -d DEF_TFF-SF_stringent/ -p profiles_TFF-SF_stringent/ -o macsyfinder_Archaeal-T4P --db-type ordered_replicon --sequence-db sequence.fasta Archaeal-T4P
 ```
 
 ## Final models
 
-For T2SS Tad T4aP ComM
+For T2SS Tad T4aP T4bP MSH ComM
 
 ```
-macsyfinder -w 4 -d DEF_TFF-SF_stringent/ -p profiles_TFF-SF_stringent/ -o macsyfinder_T2SS-Tad-T4P-T4bP-MSH-ComM --db-type ordered_replicon --sequence-db sequence.fasta T2SS Tad T4P ComM
+macsyfinder -w 4 -d DEF_TFF-SF_final/ -p profiles_TFF-SF_final/ -o macsyfinder_T2SS-Tad-T4P-T4bP-MSH-ComM --db-type ordered_replicon --sequence-db sequence.fasta T2SS Tad T4P T4bP MSH ComM
 ```
 
 For Archaeal-T4P
 
 ```
-macsyfinder -w 4 -d DEF_TFF-SF_stringent/ -p profiles_TFF-SF_stringent/ -o macsyfinder_Archaeal-T4P --db-type ordered_replicon --sequence-db sequence.fasta Archaeal-T4P
+macsyfinder -w 4 -d DEF_TFF-SF_final/ -p profiles_TFF-SF_final/ -o macsyfinder_Archaeal-T4P --db-type ordered_replicon --sequence-db sequence.fasta Archaeal-T4P
 ```