Update README.md

README.md

@@ -10,12 +10,10 @@ The pipeline is basically written in perl.
 ## How does it work?
 It requires an important number of pre-computed datasets: 
 - A Core Genome built with 3 clades and its Phylogenetic reconstruction:
-    - The clade of interest
-    - Two clades, outgroups of the clade of interest.
+    - The clade of interest (Query)
+    - Two clades, outgroups of the clade of interest (Close and Distant).
 
-Each core-gene alignment has to be divided by clade, so we can distinguish between the clade of interest and the outgroups. *The core genes for the three clades must be formated as HMMer database*
-
-- The Multiple sequence alignments of each Core-Gene
+- Each core-gene alignment has to be divided by clade, so we can distinguish between the clade of interest and the outgroups. *The core genes for the three clades must be formated as HMMer database*
 - A list of reference sequences
 - A folder with the metagenomic datasets