jule_todo_turtles.txt

- look at functions of species outlier genes per habitat in general not only GO enriched / think about g:profiler
- WES: I just thought that it would be better to calculate the pure distances based on the filtered/trimmed alignments!!! I will send data that is input to codeml

DONE:
- change n_seg_sites to n_parsimony_sites -> only 304806at32523 : 9
- methods on removing outgroups, filtering for enough taxa, dN dS workflow
- improve Fig1, Fig2, Fig3


EXPLANATIONS:

dN/dS: ZEROs
- calculating dN/dS: before changing zeros! put NAs everywhere where either dN or dS has 0, after filled with valid dN/dS ratios, fill NAs with means (as before) and then log

STEPS: 
- impute
- log
- transpose

OR:
- impute
- transpose
- log

but always impute before transpose: otherwise not the same size
and alwase impute before log: otherwise different scale for taking the mean