csubst inspect

csubst inspect

csubst inspect writes branch maps, tree plots, alignment exports, and ancestral-state tree plots without calculating convergence statistics. It is useful for checking how CSUBST interprets an input dataset before or after running csubst search.

Minimal command

csubst inspect \
  --alignment_file alignment.fa.gz \
  --rooted_tree_file tree.nwk \
  --foreground foreground.txt

When to use it

Use csubst inspect when you want to:

• confirm branch IDs used by csubst search and csubst sites
• inspect foreground and marginal branch assignments
• export codon and amino-acid alignments after CSUBST input loading
• generate ancestral amino-acid or codon state tree PDFs
• check 3Di recoding inputs and smoke-test structural-alphabet workflows

Common options

• --plot_state_aa no|all|SITE_SPEC
• --plot_state_codon no|all|SITE_SPEC
• --species_regex
• --species_overlap_node_plot
• --plot_nonsyn_recode_pca
• --download_prostt5

For the full option list, run:

csubst inspect -h

Output files

By default, csubst inspect writes into csubst_inspect/. Common outputs include:

• csubst_alignment_codon.fa
• csubst_alignment_aa.fa
• csubst_tree.nwk
• csubst_branch_id.pdf
• csubst_branch_map.tsv
• selected ancestral-state tree PDFs

Related pages

• Inspect outputs and ancestral state tree plots
• Foreground specification
• csubst search
• csubst sites