Protein parsimony algorithm

Description

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

Protein parsimony algorithm estimates phylogenies from protein sequences using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished.

Parameters

  • Number of times to randomise (protpars parameter -njumble )
  • Random number seed between 1 and 32767 (must be odd) (protpars parameter -seed )
  • Species number to use as outgroup (protpars parameter -outgrno )
  • Use threshold parsimony (protpars parameter -dothreshold )
  • Threshold value (protpars parameter -threshold )
  • Use which genetic code (protpars parameter -whichcode )
  • Write out trees to tree file (protpars parameter -trout )
  • Print data at start of run (protpars parameter -printdata )
  • Print out tree (protpars parameter -treeprint )
  • Print steps at each site (protpars parameter -stepbox )
  • Print sequences at all nodes of tree (protpars parameter -ancseq )
  • Use dot differencing to display results (protpars parameter -dotdiff )
  • Collect a log file
  • For more details, please check the manual page of fprotpars command.

    Input and output

    Input is a protein multiple sequence alignment.

    Output consists of two files containing. One containing a human readable output report (protpars.out.txt ) and a treefile (protpars.tree.txt) that can be used as an input for tree drawing tools (Plot an unrooted tree, Plot cladogram).