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).