@@ -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*
