Notebooks

1. expectations_analysis.ipynb - Expected mutations analysis. Contains (1) estimation of synonymous mutations counts in invariable positions; (2) calculation of expected mutations counts (used in calculation of mutation spectra) taking into account invariable positions
2. mammals_spectra.ipynb - Mammals spectra: compare different approaches of spectra reconstuction
3. position_analysis.ipynb - Selection exploration on Human and Mouse spectra (position-specific) on genes cytb, cox1, nd1 using novel method based on simulation of neutral evolution
4. alisim_analysis_sp.ipynb - Analysis of simulated by iqtree2 -alisim random spectra on random trees (Figure 1 in the paper)
5. alisim_analysis_mam.ipynb - Analysis of simulated by iqtree2 -alisim random spectra on big mammals tree (Figure 2 in the paper)
6. prepare_beasts_datasets.ipynb - Beast dataset preparation for NeMu pipeline execution. Extract mitochondrial genes from MIDORI database for different taxa and select outgroup sequence for each species-gene
7. collect_spectra.ipynb - collect ann preanalyse spectra of mitochondrial genes of vertebrates
8. prepare_nt_taxid.ipynb - analyse taxids of the nt database
9. polymorphism_compare.ipynb - compare mitochondrial genes spectra of vertebrates, calculated by NeMu, with spectra, calculated by simple consensus-based approach
10. prepare_taxa_table.ipynb - - choose taxids that used as input for the pipeline on the webserver when nt database choosen