Phylogenetic Tree Builder & Newick Viewer
Build a neighbour-joining tree with bootstrap support, or open a Newick file somebody sent you.
Paste sequences in FASTA or a tree in Newick and get a phylogenetic tree. Unaligned sequences are aligned here with center-star first; an alignment you already made is used as given; a Newick file is drawn as it stands, branch lengths and support labels included. Trees from sequences are neighbour-joining on Jukes–Cantor (DNA) or Poisson-corrected (protein) distances, rooted at the midpoint of the longest tip-to-tip path, and every branch carries the percentage of 100 bootstrap replicates that recovered it. Download the tree as Newick or export the figure as SVG, PNG or PDF. Everything runs in your browser — no sequence, alignment or tree is uploaded.
How to use the Phylogenetic Tree tool
- 1Paste three or more sequences in FASTA (aligned or not), or a Newick tree, then click Draw tree.
- 2Read the branch support: the number at a fork is the percentage of bootstrap replicates that recovered that grouping, and below about 70 it is not evidence.
- 3Download the tree as Newick, or export the figure as SVG, PNG or PDF.
Frequently asked questions
What can I paste in?
Three or more sequences in FASTA, or a tree in Newick. If the sequences are not aligned they are aligned here with center-star before the tree is built; if they already carry gaps and are all the same length, your alignment is used as it stands rather than being realigned. A Newick file is drawn as given — the page does not re-root it.
What do the numbers on the branches mean?
The percentage of bootstrap replicates that recovered that grouping. Each replicate draws the same number of alignment columns at random with replacement, rebuilds the tree, and the number counts how often the branch came back. Below about 70 the grouping is not evidence. A branch with no number is one nothing has tested — either the tree came from a Newick file with no support labels, or the alignment was too large to resample 100 times in a browser tab, which the caption says.
Is this a maximum-likelihood tree?
No. It is neighbour-joining on corrected distances — Jukes–Cantor for nucleotides, the Poisson correction for protein — which is what MEGA and Clustal draw by default. For a maximum-likelihood tree with model selection, use IQ-TREE or RAxML and bring the Newick back here to draw and export it.
Does my alignment leave the browser?
No. The alignment, the tree, the bootstrap and the figure are all computed in this tab. If you want MAFFT or MUSCLE instead of center-star, the MSA Viewer runs those on the server and its result pastes straight back in here.