## 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).