csubst sites

csubst sites

csubst sites summarizes site-wise substitution and convergence patterns for selected branches or branch sets. It is usually run after csubst search, once you have chosen branch IDs or branch combinations to inspect.

csubst site remains available as a legacy alias, but the wiki uses csubst sites.

Minimal command

csubst sites \
  --alignment_file alignment.fa.gz \
  --rooted_tree_file tree.nwk \
  --branch_id 23,51

When to use it

Use csubst sites when you want to:

• inspect which sites drive a convergence signal
• compare substitutions in selected branch pairs or branch sets
• visualize branch IDs and high-scoring sites on a tree
• run lineage-mode or set-mode site summaries
• map convergent substitutions onto protein structures with --pdb

Main modes

• intersection: summarize combinatorial substitutions in selected branches
• lineage: summarize substitutions along an ancestor-to-descendant path
• set,SUBTYPE,EXPR: use set algebra over branch-wise substitution support

The default mode is intersection.

Output files

csubst sites writes branch-set-specific job directories such as:

• csubst_sites.branch_id23,51
• csubst_sites.lineage.branch_id63,2
• csubst_sites.set.any.expr23_minus_51

Common files inside a site-job directory include:

• csubst_sites.tsv
• csubst_sites.pdf
• csubst_sites.tree_site.pdf
• csubst_sites.tree_site.tsv
• csubst_sites.outputs.tsv

For output interpretation, see: Interpreting output files of csubst sites

Related pages

• csubst sites modes
• Mapping convergent substitutions on protein structures
• Inspecting spurious convergence using csubst sites
• csubst search
• csubst inspect