In the current implementation, --fg_clade_permutation should be combined with --exhaustive_until to randomize branch combinations properly. If this requirement is not fulfilled, CSUBST reports it as below. CSUBST should re-calculate missing branch combinations in the future version even with --exhaustive until 1.
Command:
CSUBST command: csubst analyze --max_arity 3 --threads 4 --alignment_file alignment.fa --rooted_tree_file tree.nwk --iqtree_redo no --fg_exclude_wg no --fg_stem_only no --fg_format 2 --foreground foreground.tsv --exhaustive_until 1 --fg_clade_permutation 1000
CSUBST working directory: /Users/kf/Dropbox/repos/csubst/data/GH19_chitinase_tiny
Stdout:
21 (24 - 3) permuted foreground branch combinations were dropped because they were not included in the cb table.
In the current implementation, --fg_clade_permutation should be combined with --exhaustive_until to randomize branch combinations properly. If this requirement is not fulfilled, CSUBST reports it as below. CSUBST should re-calculate missing branch combinations in the future version even with --exhaustive until 1.
Command:
Stdout: