Phylogenetic tree maker (UPGMA)
Paste two or more sequences in FASTA format and the tree maker aligns them, calculates corrected distances, and builds a UPGMA tree. You get the tree, the distance matrix, the merge steps in order and the tree as a Newick string you can open in other software.
What you get
- A UPGMA tree from 2 to 100 sequences
- A multiple alignment and Jukes-Cantor corrected distances for DNA
- The distance matrix and the UPGMA merge steps, one by one
- The tree as a Newick string
How to use it
- Open the Tree tab and paste your sequences as FASTA, one record per sequence.
- Build the tree.
- Read the clusters from the tips inward, and copy the Newick string if you need it elsewhere.
Worked example
Four short sequences, A to D, in FASTA:
>A
ATGGCTAAGCTTGAATTC
>B
ATGGCTAAGCTAGAATTC
>C
ATGGCCAAGCTAGAGTTC
>D
ATGACCAGGTTAGAGTTAThe tree comes out as the Newick string:
(D:0.20876,(C:0.07719,(A:0.02886,B:0.02886):0.04833):0.13157);A and B are the closest pair and join first; C joins next and D is the outermost branch.
Limits to know about
- At least 2 and at most 100 sequences.
- UPGMA assumes a constant rate of change across branches, so it suits quick, teaching-style trees more than careful evolutionary studies.
Common questions
What is UPGMA?
A method that repeatedly joins the two closest groups and averages the distances. The phylogenetics guide walks through it step by step.
What is a Newick string?
A compact text format for a tree: nested brackets for groups and numbers for branch lengths. Most tree viewers can read it.
Do the sequences need to be aligned first?
No. The tool aligns them for you before it measures distances.
Are my sequences stored?
No. Sequences are processed in memory to produce your result and are not stored or logged. The privacy policy has the details, including what BLAST sends to NCBI and EMBL-EBI.