Clade Desk - your alignment and your Newick tree, checked and figure-ready

Paste a FASTA alignment, its Newick or NHX tree and a few lines of run notes, and get the review a phylogenetics referee would give it. Three lanes over one analysis: alignment quality control with 1-based column ranges to keep and drop, a per-taxon keep / trim / drop / resequence call and a trimming recipe; a tree and support audit that grades every clade against the correct threshold for the support method you actually ran; and a journal figure specification with panel sizes in millimetres, a colourblind-safe palette, display rules and a caption. A free in-browser Newick and FASTA reader parses both files first, draws the tree as a phylogram or cladogram, and measures column occupancy, informative sites, gap and ambiguity fractions, polytomies, negative branch lengths, the support distribution and whether the tree's taxon set matches the alignment's - then every one of those facts is reconciled against the model's answer. IQ-TREE's combined SH-aLRT/UFBoot labels are read as two series against two thresholds. Derived from three agent skills: @k-dense-ai/etetoolkit, @k-dense-ai/scikit-bio and @k-dense-ai/scientific-visualization. Not affiliated with those skills' authors or with any journal named in the figure lane.

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