## PDNA parsimony algorithm

### Description

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

DNA parsimony algorithm estimates phylogenies by the parsimony method using nucleic acid sequences. It allows use the full IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps are treated as a fifth nucleotide state. It can also be used for transversion parsimony. This method can cope with multifurcations, reconstruct ancestral states, use 0/1 character weights, and infer branch lengths.

### Parameters

- Number of trees to save (fdnapars parameter -maxtrees )
- More thorough search (fdnapars parameter -thorough )
- Rearrange on just one best tree (fdnapars parameter -rearrange )
- Use transversion parsimony (fdnapars parameter -transversion )
- Number of times to randomise (fdnapars parameter -njumble )
- Random number seed between 1 and 32767 (must be odd) (fdnapars parameter -seed )
- Species number to use as outgroup (fdnapars parameter -outgrno )
- Use threshold parsimony (fdnapars parameter -dothreshold )
- Threshold value (fdnapars parameter -threshold )
- Write out trees to tree file (fdnapars parameter -trout )
- Print data at start of run (fdnapars parameter -printdata )
- Print out steps in each site (fdnapars parameter -stepbox )
- Print sequences at all nodes of tree (fdnapars parameter -ancseq )
- Print out tree (fdnapars parameter -treeprint )
- Use dot differencing to display results (fdnapars parameter -dotdiff )
- Collect a log file

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

### Input and output

Input is a dna multiple sequence alignment.

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