## Nucleic acid distance algorithm

### Description

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.

### Parameters

- Choose the method to use (fdnadist parameter: -method)
- Gamma distribution (fdnadist parameter: -gammatype)
- Number of substitution rate categories (fdnadist parameter: -ncategories)
- Category rates (fdnadist parameter: -rate)
- Coefficient of variation of substitution rate among sites (fdnadist parameter: -gammacoefficient)
- Fraction of invariant sites (fdnadist parameter: -invarcoefficient )
- Transition/transversion ratio (fdnadist parameter: -ttratio )
- Use empirical base frequencies from seqeunce input (fdnadist parameter: -freqsfrom )
- Base frequencies for A C G T/U (use blanks to separate\) (fdnadist parameter: -basefreq )
- Output as a lower triangular distance matrix (fdnadist parameter: -lower )
- Output as a human-readable distance matrix (fdnadist parameter: -humanreadable )
- Print data at start of run (fdnadist parameter: -printdata )
- Collect a log file

For more details, please check the manual page of fdnadist command.

### Input and output

Input is a nucleotide multiple sequence alignment.

Output is a text file containing the distance matrix.