The Concatenation-Based Phylogenomic Approach is Incapable of Illustrating the complicated Evolutionary History of Staphylococci

The files in this folder are all original data used in our work about in-depth phylogenomic analysis of Staphylococci.

• species tree: all species trees.

  This folder contains two subfolders

  1. rooted

     • ST_sm_no_outgroup_unroot.treefile: An unrooted species tree based on super-matrix method for Staphylococci without outgroups.

     • ST_sm_outgroup_unroot.treefile: An unrooted species tree based on super-matrix method for Staphylococci with outgroups.

     • ST_st_no_outgroup_unroot.treefile: An unrooted species tree based on super-tree method for Staphylococci without outgroups.

     • ST_st_outgroup_unroot.treefile: An unrooted species tree based on super-tree method for Staphylococci with outgroups.

  2. rooted

     • r3.tree: a species tree rooted at branch 3

     • r5.tree: a species tree rooted at branch 5

• gene trees: all gene trees of 660 SOGs.

  This folder has a hierarchical structure:

   ├── recombination_corrected
   │   ├── no_outgroup
   │   └── outgroup
   ├── rooted
   │   ├── no_outgroup
   │   │   ├── IQ_MAD_General_Model
   │   │   ├── IQ_MAD_Mixture_Model
   │   │   ├── IQ_MID_General_Model
   │   │   ├── IQ_MID_Mixture_Model
   │   │   ├── MB_MAD
   │   │   └── MB_MID
   │   └── outgroup
   │       ├── IQ_MAD_General_Model
   │       ├── IQ_MAD_Mixture_Model
   │       ├── IQ_MID_General_Model
   │       ├── IQ_MID_Mixture_Model
   │       ├── MB_MAD
   │       └── MB_MID
   └── unrooted
       ├── no_outgroup
       │   ├── IQ_General_Model
       │   ├── IQ_Mixture_Model
       │   └── MB
       └── outgroup
           ├── IQ_General_Model
           ├── IQ_Mixture_Model
           └── MB

• sample of trees: this fold contains the bootstrap trees of all orthogroups (more than three sequences) inferred by Orthofinder for ALE estimation.

• mrbayes_sample_trees. This fold contains the mcmc sample trees of two run chains (run1 and run2) by Mrbayes for 660 SOGs.