Phylogenetic Tree Builder

Advanced

Pipeline Configuration

Currently: MAFFT + IQ-TREE five-iteration search, terminal overhang trim, midpoint-rooted, SH-aLRT branch support (1000 replicates, not bootstrap).

Alignment Method

Choose the algorithm for multiple sequence alignment.

Fix sequence orientation Reverse-complement any sequence that was submitted backwards. A single reversed sequence is enough to wreck an alignment and the tree built from it.

Trimming Method

Remove poorly aligned regions to improve signal. The default drops columns that are more than 90% gaps, which clears alignment junk while leaving the variable ITS1/ITS2 regions intact.

Trim terminal overhangs Remove low-coverage alignment ends before the selected trimmer and tree builder. Terminal runs of unknown bases (N) do not count as genuine coverage.

ITS Region

Detect the chosen subregion with ITSx profiles and align only that region, so every sequence covers the same stretch of the locus. Sequences without enough of the target region are dropped and listed under the tree.

Tree Inference

Program

Substitution Model

E.g., GTR+G, JC69, HKY.

Bootstrap Replicates

Phylogenetic Tree Builder

Add Sequences

Provisional Species Names:

Sequence queue

Pipeline Configuration

Tree Inference

Phylogenetic Tree Builder

Add Sequences

Provisional Species Names:

Sequence queue

Pipeline Configuration

Tree Inference

Filter by BLAST Metrics

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