Tree Explorer

Tree, alignments and per-position charts for a clade, at the positions you chose.

Tree

Clade level

Clade

Group clades by

Alignment positions (E. coli numbering)

# ⓘ

16S

23S

Whole rRNA: · ·

Preset

Find positions near… (3D shell)

Fills the 5S, 16S and 23S boxes above with every nucleotide that has any heavy atom within the radius of any heavy atom of the center, measured in the E. coli 70S structure PDB 7K00. Both subunits are searched, so a shell can cross the interface.

Preset Center Chain then positions; separate chains with ;. Chains: 5S, 16S, 23S (E. coli numbering), mRNA (7K00: A-site codon 19–21, P-site 16–18), A-tRNA, P-tRNA (tRNA numbering; anticodon 34–36). Radius (Å)

Advanced settings

Posterior probability threshold

How confident Infernal must be that a base belongs in its column. Bases below the cutoff are left out of the consensus and drawn lighter in the alignment.

rRNA copies per species

Top hit: one sequence per species, the best rRNA hit in its genome. All hits: every copy. The charts then count every rRNA, a species row is the consensus of its copies, and a clade row the consensus of its species' consensuses (each species counts once). Insertion frequency and insertion carets then count copies too (“Insertion in 3 of 10 copies”).

Entropy scale

Y axis of the Shannon entropy plot. Log separates the nearly invariant positions; linear shows differences between variable ones. Redraws without re-running.

Deletion & insertion scale

Y axis of the deletion and insertion frequency plots. Log runs from 0.1% to 100% and spreads out rare deletions and insertions; anything at or below 0.1% sits on the baseline. Redraws without re-running.

Clade insertion caret threshold (%)

For grouped trees: a clade row gets an insertion caret only where at least this % of its species have one. 0 = any species.

Panels to show

Tree & alignments Base composition Shannon entropy Deletion frequency Insertion frequency Domain consensus Clade consensus

Unticked panels are skipped, which speeds up Generate. The tree is the slowest part.

Base Composition

A U G C Ambig Poor Share of each base at a position; gaps left out

Shannon Entropy

Variability of A/U/G/C, in bits; * = below 0.001 bits

Deletion Frequency

Share of sequences with a deletion; missing and fragmented sequences left out

Insertion Frequency

Share of sequences with an insertion after the position; missing and fragmented sequences left out

Domain Consensus

Clade Consensus