Home

CSUBST Wiki

Setting up

Installation and test run

Dependency

Preparing CSUBST inputs

CSUBST commands

• csubst dataset: generate bundled example datasets
• csubst doctor: validate inputs and inferred IQ-TREE paths
• csubst search: calculate convergence statistics (csubst analyze is a legacy alias)
• csubst scan: list foreground recurrent amino-acid/state substitutions with rate-enrichment tests
• csubst inspect: write branch maps, tree plots, alignments, and ancestral-state plots
• csubst sites: inspect site-wise substitution patterns (csubst site is a legacy alias)
• csubst simulate: simulate codon alignments under convergent scenarios
• csubst benchmark: compare csubst search settings on the same input
• csubst benchmark-plot: plot and summarize benchmark outputs

Search guides

Foreground specification

Codon frequency estimation

Interpreting output files of csubst search

Analysis of higher-order convergence

Parallel processing and performance tuning

Benchmarking search settings

Site inspection and structures

Interpreting output files of csubst sites

csubst sites modes

Mapping convergent substitutions on protein structures

Inspecting spurious convergence using csubst sites

Simulation and inspection

Simulating molecular convergence

Inspect outputs and ancestral state tree plots

Misc

How ω and ω_C are different

FAQ