## Protein distance algorithm

### Description

This tool is based on EMBOSS command fprotdist that is a wrapper command for command protdist of the PHYLIP package.

Protein distance algorithm computes a distance measure for aligned protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, the JTT matrix model, the PBM model, Kimura's 1983 approximation to these, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. 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 distance matrix can be used as an input for tool: Phylogenies from distance matrix by N-J or UPGMA method.

### Parameters

- Number of substitution rate categories (fprotdist parameter: -ncategories)
- Rate for each category (fprotdist parameter: -rate)
- Choose the method to use (fprotdist parameter: -method)
- Rate variation among sites (fprotdist parameter: -gammatype)
- Coefficient of variation of substitution rate among sites (fprotdist parameter: -gammacoefficient)
- Coefficient of variation of substitution rate among sites (fprotdist parameter: -invarcoefficient )
- Choose the category to use (fprotdist parameter: -aacateg )
- Which genetic code (fprotdist parameter: -whichcode )
- Prob change category (1.0=easy) (fprotdist parameter: -ease )
- Transition/transversion ratio (fprotdist parameter: -ttratio )
- Base frequencies for A C G T/U (use blanks to separate) (fprotdist parameter: -basefreq )
- Print data at start of run (fprotdist parameter: -printdata )
- Collect a log file

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

### Input and output

Input is a protein multiple sequence alignment.

Output is a text file containing the distance matrix.