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.