Closed kfuku52 closed 3 years ago
csubst 10.8 Dataset = chitinase_tiny
# Run csubst simulate csubst simulate \ --codon_table 1 \ --alignment_file alignment.fa \ --rooted_tree_file tree.nwk \ --infile_type iqtree \ --foreground foreground.txt \ --fg_stem_only yes \ --num_simulated_site 5000 \ --convergence_intensity_factor 1 \ --background_omega 0.1 \ --foreground_omega 0.1 \ --tree_scaling_factor 0.1 \ --convergent_amino_acids random0 \ --num_partition 1 # Run IQ-TREE iqtree \ -s simulate.fa \ -te tree.nwk \ -m ECMK07 \ --seqtype CODON1 \ --threads-max 4 \ --ancestral \ --rate \ --redo # Run csubst analyze csubst analyze \ --codon_table 1 \ --alignment_file simulate.fa \ --rooted_tree_file tree.nwk \ --infile_type iqtree \ --max_arity 2 \ --foreground foreground.txt \ --fg_stem_only yes \ --force_exhaustive yes \ --asrv each \ --nslots 4
In csubst_b.tsv, Total S_sub = 2220.2881 Total N_sub = 220.7083
With --background_omega 1 --foreground_omega 1, Total S_sub = 1150.2343 Total N_sub = 1241.5797
--background_omega 1 --foreground_omega 1
With --background_omega 10 --foreground_omega 10, Total S_sub = 217.18 Total N_sub = 2173.6513
--background_omega 10 --foreground_omega 10
In 10.8, pyvolve's matrix is readjusted, and these results are consistent with the input omega parameters. The readjustment should be maintained.
csubst 10.8 Dataset = chitinase_tiny
In csubst_b.tsv, Total S_sub = 2220.2881 Total N_sub = 220.7083
With
--background_omega 1 --foreground_omega 1, Total S_sub = 1150.2343 Total N_sub = 1241.5797With
--background_omega 10 --foreground_omega 10, Total S_sub = 217.18 Total N_sub = 2173.6513In 10.8, pyvolve's matrix is readjusted, and these results are consistent with the input omega parameters. The readjustment should be maintained.