Raccoon tree-qc report
Phylogenetic tree quality assessment, with temporal signal evaluation and convergence/reversion flag summaries if ancestral state files available.
Phylogenetic tree quality assessment, with temporal signal evaluation and convergence/reversion flag summaries if ancestral state files available.
Tips: 51
Tree height: 0.0815
Tips with date information: 49 / 51 — 2 tip(s) missing date and excluded from root-to-tip
Tree rooting: midpoint rooted. Use the dropdown to colour tips by trait and the slider to expand the tree vertically.
Further explore this tree in PearTree.
Root-to-tip regression can be used to visually assess the temporal signal in the phylogenetic tree. It plots the genetic distance from the root against the sampling dates of the sequences.
Primer: the slope is the estimated evolutionary rate (substitutions/site/year, using decimal-year dates), the x-intercept estimates tMRCA, R² is the fraction of variation explained by the regression, and r is the Pearson correlation coefficient. These values are sensitive to tree rooting, so an incorrect root placement can shift the inferred rate, tMRCA, and fit statistics.
Slope (rate, subs/site/year): 1.06e-03 | tMRCA (x-intercept, decimal year): 1955.389 | R²: 0.609 | r: 0.780
The following tips could not be assigned a date from the tip label (via the --tip-fields date field or the last field of the label).
They are excluded from root-to-tip regression.
Root-to-tip is plotted using the remaining 49 dated tip(s).
| tip |
|---|
| PHL008|mylona_marsh|faux_kent| |
| PHL009 |
Convergent mutations are mutations that have independently arisen multiple times across the tree.
Large numbers of convergent SNPs can indicate convergent evolution (real) OR alignment/reconstruction errors (artifacts).
Ancestral state reconstruction files must be supplied to check for convergent mutations.
No convergent mutations flagged.
Reversions are mutations that revert to a previous state observed in the tree.
If assembly references are supplied, reversions can flag potential assembly errors.
Ancestral state reconstruction files must be supplied to check for reversions.
No reversions flagged.
Signatures of human immune editing are mutations that may be influenced by the host immune system. Raccoon can check for signatures of ADAR editing (clusters of T->C mutations) and APOBEC editing (TC->TT and GA->AA mutations).
Ancestral state reconstruction files must be supplied to check for signatures of immune editing.
No immune editing signatures flagged.
Treefile: cases_background.aln.masked.fasta.midpoint_rooted.nwk
Flags Csv: cases_background.aln.masked.fasta.midpoint_rooted.phylo_flags.csv
Outdir: tree-qc
Command: raccoon tree-qc --tree examples/lhfv/masked/cases_background.aln.masked.fasta.treefile -d examples/lhfv/tree-qc --midpoint-root
Generated: 2026-03-12 19:58
Raccoon version: 1.0.2
Python: 3.14.2
Platform: Darwin 24.4.0