Phylogenetic tree maker for Newick files

What a phylogenetic tree shows

A phylogenetic tree is a hypothesis about how sequences, species, or strains are related through common ancestry. Each part of the drawing has a specific meaning, and a good figure makes those parts easy to read.

• Tips (leaves) are the sampled taxa or sequences you analyzed.
• Internal nodes are inferred common ancestors. Everything descending from one node is a clade.
• Branch lengths, when present, usually measure expected substitutions per site, or time in a dated analysis. In a phylogram the horizontal distance carries that meaning; vertical distance means nothing.
• Support values such as bootstrap percentages or posterior probabilities describe how strongly the data back each split. They label internal branches, not tips.
• A rooted tree has a direction from an ancestor to its descendants. An unrooted tree only shows which groups are separated by each branch; many inference programs write unrooted trees with three branches at the base.

The Newick format in a minute

Newick describes a tree with nested parentheses. Each pair of parentheses is an internal node, commas separate its descendants, and a semicolon ends the tree. The parser here follows the Newick grammar documented with PHYLIP and accepts the extras that real programs write.

• Topology only: ((A,B),C); groups A and B together, with C as their sister.
• Branch lengths go after a colon: ((A:0.1,B:0.2):0.3,C:0.4); Scientific notation such as 1.5e-4 works too.
• A label after a closing parenthesis names an internal node. When it is a number, as in ((A,B)95,C); the tool reads it as a support value, on a 0 to 1 or 0 to 100 scale. Paired values such as 85/72 are shown as written.
• Underscores in unquoted names become spaces, so Homo_sapiens is drawn as Homo sapiens. Names with punctuation go in single quotes, and a quote inside a name is doubled: 'O''Brien strain'.
• Text in square brackets is a comment and is skipped, including NHX [&&NHX:...] and BEAST-style [&...] annotations. Spaces and line breaks between tokens are ignored.
• If the tree cannot be read, the error message gives the line and column of the problem, such as a missing closing parenthesis.

Phylogram, cladogram, or circular layout

Use the rectangular phylogram when branch lengths matter: branches are drawn to scale and a scale bar with a rounded length shows the units. Use the cladogram when you only want to show branching order; it ignores lengths and lines up every tip, which makes long species names easier to compare. Use the circular layout for large trees with a hundred or more tips, where a rectangular figure would be very tall. It is the same tree wrapped around a circle, with tip labels rotated and flipped so none are upside down. Ladderizing sorts clades by size, which tidies the figure without changing any relationships; switching layouts in this phylogenetic tree maker never changes the topology, only the drawing. The tool scales the drawing height with the number of tips and handles trees of around 500 tips.

Reading bootstrap and posterior support

Support values answer the question "how consistently does this split appear?" Bootstrap percentages come from re-analyzing resampled alignments; posterior probabilities come from Bayesian analyses. FastTree writes local support values between 0 and 1, and IQ-TREE can write SH-aLRT and ultrafast bootstrap values together as a pair. Use the support threshold to label only the branches that pass the cutoff your field or methods section uses, and say in the figure legend what the numbers are. A commonly reported cutoff is not a proof that a clade is real, and a low value means the data are uncertain about that split, not that the opposite grouping is supported.

Common mistakes when reading or drawing trees

• Reading tip order as relatedness. Neighboring tips are not necessarily close relatives; you can rotate any node without changing the tree. Relatedness comes from the most recent shared ancestor.
• Drawing an unrooted tree as if it were rooted. The base of a tree written with three branches is arbitrary. Root it with an outgroup in your analysis, or use midpoint rooting and say so in the legend.
• Treating a cladogram as if branch lengths were meaningful. In a cladogram the horizontal positions only show order.
• Placing support values on tips, or mixing bootstrap and posterior values without saying which is which.
• Omitting the scale bar from a phylogram, so readers cannot judge how much change a branch represents.
• Using red and green alone to mark clades. The clade colors here come from the Okabe-Ito palette, which stays distinguishable for common color vision deficiencies.

Where Newick files come from, and when to use other tree viewers

Most inference programs can give you Newick. IQ-TREE writes the maximum-likelihood tree to a .treefile, RAxML-NG writes .raxml.bestTree and support trees such as .raxml.supportFBP, FastTree prints a Newick tree, and MEGA can export trees from its Tree Explorer. BEAST tree summaries from TreeAnnotator are usually NEXUS files; this tool reads the first tree in a NEXUS TREES block, including a TRANSLATE table, but treats BEAST annotations as comments. For advanced annotation, established tools are a better fit: iTOL is an online tool for displaying and annotating trees with many dataset types, FigTree is a free desktop viewer designed for BEAST output, and ggtree is a Bioconductor package that brings ggplot2-style annotation to trees in R. Use this free phylogenetic tree generator online when you need a quick Newick tree viewer and a figure-ready export in seconds, and move to those tools when you need per-tip metadata strips, images, or scripted figures.