Quick Start
The easy way: make a tree from an iNaturalist observation
- Open the Tree Builder.
- Paste an iNaturalist observation URL into Import from iNaturalist. An observation number works too.
- Click Submit, check the preview, then click One-Click Tree.
- Dikarya finds the observation's sequence and related sequences, aligns them, builds the tree, and takes you to the result.
The same box also accepts an iNaturalist username, user URL, project name, or project URL. Those inputs preview the eligible observations and can create bulk tree jobs; they do not change the simple single-observation workflow above.
Quick trees and publication trees are different jobs
The normal quick tree is for sequence identification, exploring BLAST results, seeing where an unknown collection falls, checking relationships quickly, and deciding what deserves closer investigation. It is much faster, and for routine identification the slower methods usually do not add enough practical benefit to justify running them every time.
For publication trees, use an appropriate advanced phylogenetic method such as RAxML-NG, IQ-TREE, or MrBayes rather than relying on the quick exploratory tree.
Choosing one of those programs is not a scientific shortcut. Inspect the alignment, choose models and support analyses deliberately, use a biologically appropriate outgroup, evaluate convergence where applicable, and document what you ran.
Easy to miss
Tree Viewer Tricks
Right-click + drag
Drag across empty tree background to draw a selection box. Every visible tip inside it is selected. This is the fastest way to grab a clade before opening the Alignment Viewer.
Right-drag = select
Alt/Option + right-click + drag
The box turns red. Releasing it prunes every visible tip inside, which is much quicker than removing a long run of unwanted sequences one at a time.
Alt + right-drag = prune
Right-click a branch tip or internal node
A tip menu can open its source observation, prune the clicked tip (or the current multi-tip selection), copy sequence names or iNaturalist numbers, and rename one tip. Rename 1 node appears below the prune action when no tip is selected, or when the right-clicked tip is the only selected tip. It changes the displayed tree-tip name, not the DNA sequence.
On an internal node, the menu can select descendant branches, collapse or expand the subtree, and Rotate node. Rotation only changes the order in which the branches are drawn; the topology is unchanged.
Alignment Viewer
This is the check I use most often after looking at the tree:
- Right-click and drag to select the clade or sequences of interest.
- Click Alignment Viewer (or press V).
- Inspect the aligned sequences together.
This shows which bases actually differ, whether a branch reflects meaningful substitutions, where gaps occur, and whether questionable sequence ends are driving the result. If nothing is selected, the viewer opens the sequences currently visible in the tree.
Compare cleanly
Highlight differences and Variable columns only start on. Compare to the consensus, choose a reference sequence from the menu, or click a sequence name to use it as the reference.
Narrow the view
Filter names; sort in tree order, by similarity, difference, length, or leading gaps; and optionally include pruned sequences. Copy or download the displayed records as FASTA when you want to work with that subset elsewhere.
Working with a finished tree
Pruning
Select one or several tips and click Prune, use the tip's right-click menu, or use the red Alt/Option + right-drag box. Pruning removes those tips from the working tree and from the pruned FASTA. Original Newick and Original FASTA remain available, so the input analysis is not erased.
Rename
Select one or more tips and click Rename to edit them together. For one tip, right-click it and use Rename 1 node. Renames are saved and reapplied when the tree reloads, but they change labels only—the underlying nucleotide sequence is untouched.
Rerooting
The Root menu currently offers Auto root, Midpoint root, Most divergent hit, and Manual root here. The separate Reroot button also starts manual rooting, and Midpoint applies midpoint rooting directly. Auto root uses the sequence of interest when Dikarya can identify it; the viewer lets you set that focal tip when it cannot.
A convenient display root on an exploratory BLAST tree is not evidence of the true evolutionary root. For publication work, choose an outgroup based on the biology.
Rotate, collapse, sort, and color
Rotate node, subtree collapse, and node sorting make a crowded tree easier to read without changing its topology. Color groups and quick color swatches save highlights on selected tips, which is handy for marking collections, clades, types, or sequences you want to discuss later.
Recompute
Prune first, then use Recompute when you want Dikarya to realign the remaining sequences and infer a new tree. This recalculates topology, branch lengths, and support; it is more than a redraw. Renames and the pruned-taxa list are kept. Recompute is usually unnecessary after a display-only rename, color, rotation, or reroot.
Other ways to start a tree
These are useful when the One-Click Tree is not the right starting point.
iNaturalist
Use an observation ID or URL for one collection. A username, user URL, project name, or project URL previews eligible observations and can queue bulk tree jobs. A single observation can also be sent to NCBI BLAST or Mycomap BLAST before you add results to the queue.
Mushroom Observer
Paste a current, short, or legacy Mushroom Observer observation URL, or just its number. When ITS sequence data are available, choose the sequence and BLAST it, add it to the queue, or use One-Click Tree.
Mycomap BLAST results
Paste a Mycomap BLAST Results URL. Choose NCBI Results, Local Results, or both, and optionally remove duplicates or filter conflicting local FASTA records. You can fetch sequences into the queue or run a One-Click Tree directly.
BLAST
Paste one DNA sequence or GenBank accession into BLAST for Related Sequences. Set the minimum identity and choose 10, 50, 100, or 200 maximum results, then add the useful hits to the queue.
FASTA
Paste FASTA into Add Custom Sequences, or upload a .fa,
.fasta, .fna, or .txt file.
>My_sequence
ACGTACGTACGT...
>Another_sequence
ACGTACGTACGT...GenBank accessions
Paste one or more accessions into Add Custom Sequences. This is useful for adding named reference sequences or rebuilding a sequence set from a paper. The form can also append GenBank collection locations to the FASTA headers.
Sequence Queue
The queue matters mostly when you are not using the single-observation One-Click Tree. It lets you combine your own FASTA with iNaturalist, Mushroom Observer, GenBank, NCBI BLAST, and Mycomap records before starting an analysis.
Use the × beside a sequence to remove it or Clear All to empty the queue. The queue can be downloaded as FASTA. When imported Mycomap records include metrics, Filter can screen them by query coverage, subject coverage, and identity. The star checkbox marks a queued sequence as an outgroup for a RAxML-NG run.
Adding sequences to an existing tree
From an editable finished tree, click Add Seq. Dikarya opens the Tree Builder with the current unpruned sequence set already in the queue. Add or remove records from any of the normal sources, then click Add & Recompute. The advanced panel is prefilled from the job; leave it alone to reuse those settings, or change it deliberately for the new run.
Downloads
The finished tree toolbar exposes the files that exist for that analysis:
- Original Newick and Current Newick for the untouched and currently displayed trees.
- NEXUS Tree, using the edited/pruned NEXUS tree when one exists.
- Original FASTA and Pruned FASTA.
- Aligned FASTA (Before Trimming) and, when applicable, Trimmed FASTA (Tree Input).
- Trimming Inspection ZIP when a trimming report was produced; it includes before/after FASTA and a marked HTML report.
- MrBayes Analysis Files for MrBayes jobs, including commands, parameter/tree traces, and summaries.
- Download SVG and Download JPG for a picture of the displayed tree.
For publication work, keep the alignment, tree, trimming report, and program output—not only a screenshot.
Advanced Tree Building
Settings for when you have a reason to change them
You do not need these settings for routine One-Click Trees.
Alignment
MAFFT (Default) is the normal choice. MUSCLE and Clustal Omega are available, and None - Skip Alignment (Use as-is) is for input that is already aligned. The ITS Region control can extract ITS1, 5.8S, ITS2, or full ITS with ITSx before alignment; sequences without enough of the requested region are dropped and reported below the tree.
Trimming
The default is trimAl gap-threshold (recommended), which removes columns that
are more than 90% gaps. You can choose no trimming, trimAl -automated1, or BMGE;
terminal-overhang trimming is a separate control. The interface specifically warns that
-automated1 can remove informative ITS1/ITS2 regions. Automated trimming is not
automatically correct—inspect important alignments in the Alignment Viewer and retain the
Trimming Inspection ZIP when it is available.
FastTree 2.2.0 (Fast ML)
This is the quick method and my normal exploratory choice. It is fast and useful for identification. Dikarya runs nucleotide GTR+CAT/Gamma settings and reports FastTree's SH-like local support from 1,000 resamples; those values are not bootstrap proportions or Bayesian posterior probabilities.
RAxML-NG (High Quality ML)
RAxML-NG performs maximum-likelihood inference. Dikarya groups the main run choices into Fast but Good, Standard, Publication, and Maximum presets, which change starting-tree counts and early stopping. Its bootstrap controls use AutoMRE with selectable replicate caps, and this is the method that exposes the queued outgroup selector.
IQ-TREE (Maximum Likelihood)
IQ-TREE is another maximum-likelihood option. ModelFinder is the recommended
model choice in the form and selects by BIC; fixed and custom models are also available.
Dikarya exposes Ultrafast Bootstrap and SH-aLRT replicates and labels nodes
SH-aLRT/UFBoot when both are run.
MrBayes (Bayesian)
MrBayes uses Bayesian phylogenetic inference. The form exposes generations, independent runs, chains per run, and burn-in. More generations do not by themselves make a result reliable: inspect the downloaded parameter traces and summaries for convergence and effective sample size, and report how convergence was assessed.
Models, support, and rooting
A substitution model describes how sequence changes are treated. Bootstrap, UFBoot, SH-aLRT, SH-like support, and posterior probabilities are program-specific measures; none is proof that a taxonomic conclusion is correct. For serious phylogenetic work, select an appropriate outgroup and explain why. Automatic and midpoint roots are useful display choices for exploratory trees, not substitutes for that biological decision.
Neighbor Joining (Fast) is also available as a simple distance-based option, but it is not the default exploratory method or one of the publication-oriented choices above.
API and Automation
Dikarya has a public API for scripts, other websites, and applications. It can submit and list jobs, check status or stream events, retrieve files and logs, recompute or edit trees, and call supported sequence tools including BLAST and GenBank lookup. The API also supports the single-observation iNaturalist One-Click Tree workflow.
Most API calls use a scoped token in the Authorization: Bearer dikarya_... header. Sign in
to mint a token, copy its secret when it is shown, and grant only the scopes the script needs.
Token management requires a Dikarya login.
Practical rule of thumb
For sequence identification: paste the iNaturalist URL → Submit → One-Click Tree → inspect the tree → select the interesting clade → Alignment Viewer.
Start changing alignment methods, trimming methods, evolutionary models, support settings, or tree-building programs when you have a reason to. For publication trees, use an appropriate advanced phylogenetic method, inspect the alignment carefully, retain the underlying files, and report the analysis settings.
Help and feedback
If something is confusing, a tree looks wrong, you find a bug, or you have an idea that would make Dikarya more useful, please let me know. Alan Rockefeller reads the messages and the public suggestion list. Email: alanrockefeller [at] gmail [dot] com.