This tool is based on EMBOSS command fdnadist that is a wrapper command for command dnadist of the PHYLIP package.
Nucleic acid distance algorithm can be used to compute four different distances between species from nucleic acid sequences. The distances are the Jukes-Cantor formula, one based on Kimura's 2- parameter method, the F84 model used in DNAML, and the LogDet distance. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences.
The resulting distance matrix can be used as an input for tool: Phylogenies from distance matrix by N-J or UPGMA method.
For more details, please check the manual page of fdnadist command.
Input is a nucleotide multiple sequence alignment.
Output is a text file containing the distance matrix.