Welcome to the orthocore wiki!

Given a set of bacterial genomes, orthocore is a perl pipeline that allows you to obtain the core genome set and use it to construct a phylogenomic tree. Phylogenomic trees may provide better resolution than single locus trees.

Orthocore perform the following tasks:

1. Obtain best hits for each gene (blastp)
2. Obtains a list of best bidirectional hits
3. Align (MUSCLE)
4. Shave (Gblocks)
5. Concatenates
6. Gives you a quicktree and a matrix
7. Aditionally you can consult functions.