Intro

This is a work-in-progress repository

Workflow

This is a general workflow for ancestral reconstruction with links/tags to more detailed sections

1. Genome_selection First we select the genomes to use and download from NCBI/collect. This includes checking completeness checkm2_results and average nucleotide identity fastani_results #completeness #ani

2. Annotation Genomes here annotated using MetaErg2
   #metaerg #annotation

3. Species Tree

   1. Tree_of_mags a. tree_of_mags uses conserved single copy marker gene HMMs - same as used gtdb ~ 50. e.g, rRNA, etc
   2. Run raxml (a bit time-consuming)
   3. Reroot the species tree

4. Gene trees

   1. Finding Orthologs a. this is essentially a homology search. This script is going to produce 1000s of clusters of orthologs and paralogs
   2. Run MSA using clustalo
   3. IQtree fast bootstrap to produce gene trees
   4. Convert everything into ALEobjects

5. Gene-tree-species-tree Reconciliation