What's New

Recent updates, improvements, and new features in Dikarya tree builder.

New Improvement

Graceful MycoMap BLAST backlog handling

When MycoMap’s NCBI BLAST queue is backed up, Dikarya now recognizes queued searches, builds from available local MycoBLAST hits, reports queue position, and checks hourly to add NCBI results later without flooding errors.
New Fix

NEXUS tree downloads now open in other software

Downloaded NEXUS trees were written with unquoted taxon labels, so any label containing a space, comma or parenthesis — which is most fungal labels — produced a file that FigTree, PAUP* and other NEXUS readers refused to parse. Labels are now quoted and referenced by number, the way MrBayes and PAUP* write them. Pruning or rerooting a tree also no longer rounds very short branches down to exactly zero, which had made distinct sequences look identical in downloads.
New Improvement

MrBayes now stops when your runs converge

Bayesian trees no longer run for a fixed 50,000 generations. The generation count is now a maximum — the default is 1,000,000 — and MrBayes ends the run as soon as the independent runs agree, when the average standard deviation of split frequencies drops below 0.01. Short analyses finish about as fast as before, while datasets that needed longer actually get it: the old 50,000-generation default routinely finished with an effective sample size near 10, far below the usual floor of 200. Every run is now checked afterwards for ASDSF, PSRF and ESS, and a run that misses those thresholds is flagged instead of quietly reported as finished. You can turn early stopping off with a checkbox under Advanced Options to force the full run.
New Feature

Analyze your tree with Claude

The tree viewer has a new Analyze with Claude button. It reviews your finished alignment and tree and reports back on how trustworthy the result is — an overall verdict, what the analysis got right, ranked concerns, concrete recommendations, and specific sequences worth a second look.

It is careful about what it is judging: your sequences are never sent anywhere. Every statistic — column occupancy, parsimony-informative sites, support distribution, branch-length outliers, duplicate groups — is computed here on the server, and only that summary is reviewed. It also reads support values on the correct scale, so a FastTree SH value of 0.78 is not mistaken for a 78% bootstrap.

Reviews are cached, so re-opening a tree you have already analyzed is instant. Editing the tree — pruning, rerooting, renaming, recomputing — produces a fresh review, and there is a Re-run button whenever you want one.
New Improvement

Mouse buttons swapped in the tree viewer

Left-drag on empty tree background now draws a selection box, and right-drag pans the tree - the reverse of the old behavior. Alt/Option + left-drag still prunes everything inside the red box, and Ctrl/Cmd + left-drag toggles selection. Clicking a tip or branch is unchanged: left-click selects, right-click opens its menu. The B keyboard shortcut for Box Select mode has been removed, since left-drag now always selects.
New Feature

Label clades on your tree with layered annotations

The tree viewer can now draw publication-style clade labels beside your tree. Right-click a branch and choose "Add clade annotation…" to label that whole clade — no need to select every tip. Annotations live on independent layers, so you can stack nested ranks such as subsections, sections and subgenera side by side, with layer 1 sitting closest to the tips. Each layer sets its own font, size, italic/bold and colours, and individual annotations can override any of them. Nested labels within one layer are placed in separate lanes so they never collide, and the canvas widens automatically so long labels are never clipped. Annotations are tied to the sequences themselves, so renaming a tip, rotating a branch or rerooting keeps them attached; pruning shrinks an annotation instead of deleting it. Everything is saved with the tree and included in SVG and JPG exports. Manage everything from the new Annotations button; people viewing a shared tree see the labels but cannot change them.
New Improvement

Download an Edited FASTA that matches your tree

The tree viewer's "Pruned FASTA" download is now "Edited FASTA". It gives you the unaligned sequences as your tree currently stands — pruned sequences removed and renamed tips carrying their new names as FASTA headers. It stays greyed out until you prune or rename something, then lights up so it's easy to find. "Original FASTA" still returns your sequences exactly as submitted.
New Feature

Import single sequences from MycoMap

You can now paste a MycoMap sequence record URL (mycomap.com/genetics/sequences/...) directly into the Tree Builder to add that one sequence to your queue. Previously only BLAST results pages were accepted, and a sequence page was rejected as an invalid URL.
New Feature

New Dikarya Help guide

A new public Help page walks through One-Click Trees, overlooked Tree Viewer gestures, the Alignment Viewer, sequence imports, downloads, advanced phylogenetic methods, and API automation, with direct ways to contact Alan or leave a suggestion.
New Improvement

Larger tree jobs and clearer failure help

Larger analyses now receive substantially more processing time and memory. If a job must be stopped, its status page explains why and provides a direct way to contact Alan with the job ID.
New Feature

GenBank collection locations in FASTA headers

When you paste GenBank accessions, or FASTA headers that contain them, the Tree Builder can now look up each record's collection location and append it to the header. A checkbox appears next to the sequence box as soon as accessions are detected. Locations come from the GenBank record itself, and for the rare records that only have GPS coordinates, the coordinates are converted to a place name. For example, "Agrocybe sp. MJ505555" becomes "Agrocybe sp. MJ505555 USA: Colorado", so tree tips show where each specimen came from.
New Improvement

IQ-TREE now selects the best-fit model automatically

New IQ-TREE trees run ModelFinder, which tests the standard substitution models and builds the tree with whichever fits best by BIC, instead of always assuming GTR+G. It typically adds only a couple of seconds, and the selected model is reported with the finished tree. You can still pick a specific model from the new dropdown if you need to match a published analysis. The Add Sequences page also keeps its Advanced panel now, pre-filled with the job's current settings, so you can change the program or parameters when you add sequences and recompute.
New Update

Phylogenetic trees now built with IQ-TREE 3

The IQ-TREE maximum likelihood engine has been upgraded from version 2.0.7 to version 3.1.3, bringing six years of upstream improvements to model selection, likelihood optimization, and multi-threading. All existing options work exactly as before, including substitution model choice, ultrafast bootstrap, and SH-aLRT branch support. Because the newer version optimizes likelihoods differently, a tree rebuilt from the same alignment may show slightly different branch lengths and support values than it did previously. This is expected and does not indicate a problem with either result.
New Feature

Build trees from ITS1, 5.8S, or ITS2 alone

Advanced options now let you align a single ITS subregion instead of the whole submitted sequence. Dikarya detects the region with ITSx profiles so every sequence in the tree covers the same stretch of the locus, instead of mixing 300 bp partial barcodes with 700 bp full-length ones. Sequences without enough of the chosen region are dropped and listed under the tree with the reason.
New Feature

Compare sequences to a reference in the Alignment Viewer

The Alignment Viewer can now compare every sequence against one you choose instead of the computed consensus. Pick a sequence from the "Compare to" menu or click its name in the alignment — a holotype, for example — and Highlight Differences plus Variable Columns Only will show exactly how the other sequences deviate from it. Similarity sorting uses the same reference.
New Feature

Voucher Label Generator is live

Create polished, print-ready specimen voucher labels with the new Voucher Label Generator at https://dikarya.us/voucher-labels.
New Improvement

Observation of interest now appears at the top

New trees place the observation of interest near the top while keeping the rest of the tree neatly organized. This only rotates branches around their connection points, like turning a mobile—it does not change which sequences are related, the tree topology, branch lengths, or support values.
New Improvement

More current MycoMap names in trees

Tree building now gives updated local MycoMap names priority over older NCBI names when the sequences match exactly, providing more accurate and up-to-date names in the finished tree.
New Feature

Tree Viewer keyboard shortcuts

The Tree Viewer now includes keyboard shortcuts: D deselects all sequences; V opens the Alignment Viewer; S cycles node sorting; B toggles Box Select mode; Ctrl/Cmd + drag toggles sequences within a selection box; Alt/Option + drag prunes sequences within a selection box; Ctrl/Cmd + Enter saves names in the Rename modal; Esc closes or cancels the current mode; and ? shows the shortcut list.
New Improvement

Smarter MycoMap sequence deduplication

Dikarya now collapses near-identical MycoMap records from the same iNaturalist or Mushroom Observer observation when they differ by fewer than five non-ambiguous bases. It keeps the longer, higher-quality barcode while preserving distinct variants for tree building.
New Improvement

Mushroom Observer is now fully supported

Mushroom Observer trees can now be generated from MO observations - they reuse Mycomap BLAST results if available, always refreshing local BLAST results and giving the option to refresh NCBI results, which is default if the sequence was added to MO over a year ago. Creating a tree from a MO observation will add a comment with the link to the tree + Mycomap BLAST results.
New Improvement

More reliable RAxML runs and clearer FASTA errors

RAxML now handles outgroups after header sanitization, MOOSE safely falls back to GTR+G for ITS/DNA analyses when needed, and invalid FASTA inputs identify the exact problem and explain how to correct it.
New Improvement

Bulk iNaturalist trees create missing MycoMap BLASTs

Username and project submissions now include observations with DNA Barcode ITS even when they do not yet have a Mycomap BLAST Results URL. Each eligible observation refreshes or creates its own MycoMap results, writes a newly created URL back to iNaturalist, waits for NCBI results when needed, and then builds its tree.
New Improvement

Count-aware right-click pruning

The Tree Viewer now shows how many nodes will be removed in the right-click Prune menu. When multiple branch tips are selected, choosing Prune removes all of the selected tips shown in that count.
New Feature

Refresh Mycomap records from the Tree Viewer

Highlight one or more tree records with iNaturalist or Mushroom Observer observation numbers, then use the right-click menu to refresh their Mycomap records. Updated Mycomap names and locations are applied to the tree.
New Feature

MrBayes burn-in controls and analysis downloads

MrBayes jobs now let you set relative burn-in (25% default) and download the full NEXUS command file plus raw parameter and tree traces for convergence assessment in Tracer. Generation details now show generations, independent runs, chains, and burn-in.
New Improvement

You can now copy multiple sequences / open multiple observations

In the tree viewer, if you select multiple sequences (by clicking on them, or right-click drag to draw a box) you can now right click on a sequence and copy all of the iNat numbers, or open all of the iNat/MO observations in separate tabs. If only one tab opens when multiple observations are selected, you need to enable pop-ups in your browser.
New Feature

Mycomap BLAST Results are no longer required for observation trees

When an iNaturalist observation has a DNA Barcode ITS field but no Mycomap BLAST Results field, Dikarya now starts the Mycomap BLAST automatically, adds the results URL to the observation, checks once a minute for NCBI results, and builds the tree when they are available.
New Improvement

Raxml-ng updated to v2.0.2

Previously we were running raxml-ng 2.0.0-beta3. The new release fixes some bugs, the most important for our use case being in the MOOSE model auto-selection.
New Improvement

Auto-rooting is smarter

Auto-root now roots on the best distinct outgroup clade rather than just a single target tip and no longer gets confused by long sequences in the alignment.
New Improvement

Tree viewer quick color presets

The Tree Viewer now has preset color swatches for marking selected sequences in one click, plus a custom-color picker that can apply any color to the current selection without naming a group first.
New Improvement

Sequences are now trimmed by default

Trimming happens at both ends until there are 3 overlapping sequences. This is conservative so we don't remove informative sites. There is a checkbox to disable trimming, and in the tree viewer if you scroll down past the tree you can see details on what was trimmed.
New Fix

MycoMap conflict filter precision

The MycoMap local FASTA conflict filter now only removes no-metric records when they share a sequence with a metric-backed query/identity conflict, reducing the risk of filtering legitimate near-identical local hits.
New Improvement

Tree Generation Details show import filters

Tree Viewer Generation Details now list MycoMap records filtered during import, including invalid, contaminant, and conflicting local FASTA records, so users can see which sequences were excluded and why.
New Fix

MycoMap local FASTA conflict filter

MycoMap imports now filter local FASTA records when the exported sequence is effectively the query sequence but the hit label or BLAST metrics indicate a different result, preventing mislabeled local hits from being added to new trees.
New Feature

Tree viewer iNaturalist number copying

The Tree Viewer right-click menu can now copy iNaturalist observation numbers from selected sequences, including multiple selected observations copied as space-separated numbers.
New Feature

iNaturalist usernames and projects in One-Click Trees

The Tree Builder iNaturalist input now accepts observation IDs, observation URLs, usernames, user URLs, project names, and project URLs. Dikarya previews how many observations are ready for tree building, skips observations that already have a Phylogenetic Tree field, and runs multi-tree batches in a lower-priority queue so one-at-a-time tree jobs stay responsive.
New Fix

Trimmed trees keep full tip labels

Trees built after trimAl or BMGE trimming now preserve the full submitted FASTA labels instead of shortening tips to accession-only labels.
New Improvement

Tree viewer node context menu actions

Right-clicking a tree node now offers Prune this node, and terminal sequence nodes also offer Copy sequence name for quick clipboard copying. When you right click you get two similar options - prune and hide. Prune deletes the sequence - hide just hides it from the tree viewer, so it'll still be there if you recompute the tree.
New Feature

Tree Viewer node rotation

The Tree Viewer now lets you right-click an internal node and choose Rotate node to reverse the displayed child-clade order without changing the phylogeny. Current Newick exports and refreshed views keep the rotated order, while Original Newick remains unchanged.
New Feature

Smarter rooting for BLAST trees: Auto root + Most Divergent Hit modes

The tree viewer now has a Root: dropdown with Auto root, Midpoint root, Root on most divergent hit, Unrooted, and Manual root here. Auto root anchors on the sequence of interest (the blue-highlighted tip on iNaturalist-imported trees, or any tip you mark with the new Set sequence of interest button) and chooses a useful display root from the most distant high-quality BLAST hit. This is a visualization heuristic, not a claim about the true evolutionary root. If no good candidate is found, Auto root cleanly falls back to midpoint rooting and tells you why.
New Fix

Tree recompute keeps pruned sequences out

Recomputing a tree from the Tree Viewer now excludes sequences that were already pruned, including sequences whose tree labels use the full FASTA header.
New Improvement

Improved Alignment Viewer highlighting

Highlight Differences in the Alignment Viewer has been visually tuned so differences stand out more clearly while keeping the alignment readable and comfortable to scan.
New Feature

Alignment Viewer in tree results

Tree results now include an interactive Alignment Viewer that opens the job's aligned sequences, follows tree selection, excludes pruned sequences by default, can optionally include pruned sequences, color-codes nucleotides, and offers sorting and difference-highlighting tools.
New Feature

Generate trees from iNaturalist observations

Dikarya can now create a one-click tree from a single iNaturalist observation that has a MycoMap BLAST Results field, then adds a Phylogenetic Tree observation field to the observation when the tree finishes. The iNaturalist observation is highlighted in blue in the tree viewer to make it easy to find.
New Improvement

Tree viewer right click menu can now open iNat / MO / MP / Genbank / Mycomap

The Tree Viewer now allows you to open observation in iNaturalist, Mushroom Observer or Mycoportal when those record types are detected. For GenBank accessions, the menu now offers both Open Sequence in GenBank and Open sequence in Mycomap. To use this feature, right click on any sequence in the tree.
New Improvement

Tree viewer adds custom color groups

The Tree Viewer now shows color groups as clickable color chips. You can create groups with a custom color, edit a group color, apply a group by clicking its chip, and each sequence now belongs to only one color group at a time. Colors persist when the page is reloaded or someone else views your tree.
New Improvement

Added a public API

Users can now generate an API key and do anything that they can do on this website from within other programs. API docs: https://dikarya.us/api/v1/docs
New Fix

Tree viewer box select allows you to rapidly prune a tree

If you hold down alt and right-drag in the tree viewer, it draws a red box - any branch tips in this red box will be deleted from the tree. This makes it really quick and easy to include just the important sequences in a tree.
New Improvement

Tree Builder design refresh

The Tree Builder now uses the new journal typography, lifted dark cards, boxed sequence inputs, and a gold-accented sequence queue with quick run controls.
New Improvement

Tree viewer Deselect button

The Tree Viewer now includes a Deselect button next to Midpoint that clears the current visible selection without changing the colors assigned to sequences / clades.
New Fix

Tree viewer rename labels persist

Renaming a selected sequence in the Tree Viewer now reapplies the saved label whenever the tree reloads, while keeping the original sequence ID for later prune, reroot, and rename actions.
New Feature

Tree viewer sequence metric sliders

The Tree Viewer now has live Query Coverage, Subject Coverage, and Identity % sliders that hide MycoMap metric-bearing sequences in the rendered tree while you drag, without changing the saved tree. This allows you to quickly remove low Query Coverage, Subject Coverage, and Identity % sequences from your tree - and see the effects of the sliders in real time.
New Improvement

MycoMap filter guidance in Tree Builder

The queue footer now explains how to use the MycoMap BLAST metrics filter and shows when metric-bearing hits are available.
New Improvement

MycoMap BLAST metrics in Tree Builder

MycoMap imports now preserve identity, query coverage, subject coverage, and source type for imported hits so the Tree Builder can display and filter by those metrics.
New Feature

GenBank accession import in Tree Builder

The Tree Builder custom sequence field now accepts one or more GenBank accession numbers and imports matching sequences directly into the queue.
New Feature

Selection set colors now persist across page reloads

When you color-code sequences in the tree viewer using selection sets, those colors are now saved automatically and restored when you revisit the page.
New Improvement

Mouse wheel now scrolls instead of zooming the tree

In the tree viewer, scrolling the mouse wheel now scrolls the page up and down rather than zooming in and out. Use the + / − zoom buttons in the toolbar to zoom.
New Feature

One-Click Tree from Mycomap URL

The Mycomap import section now has a second button next to Fetch Sequences: One-Click Tree. Paste a Mycomap BLAST result URL and click it to fetch the sequences and immediately start building a tree — no need to scroll down and click the separate One-Click Quick Tree button.
New Feature

What's New page launched

A changelog page is now available in the header. It shows recent updates and highlights anything new since your last visit.