Software for counting mutations over a tree

Question

[confusedious]

Hi everyone,

I have a nucleotide alignment in .fasta format and a phylogenetic tree for these data in .newick format.

I'd like to find some software that can count how many times each variable position in the alignment needs to change over a given tree tree (interpreting the mutations in the most parsimonious way).

Does anyone have any suggestions?

Answer 1

[confusedious]

I found that an estimation of the maximum mutation count at each position can be obtained using Fluxus Network's statistics tool after building a Median Joining network.

See: http://www.fluxus-engineering.com/sharenet.htm

Answer 2

[jhc]

This script might be useful: It displays what mutations occurred in each branch. Should be easy to modify to just count.

Answer 3

[Joseph Hughes]

You could use Mesquite or PAUP. I believe it is also possible to do this in R using the APE package.

[confusedious]

Thank you for the suggestions. I have tried with these packages, but have only been able to get a mutation count for the whole alignment/tree combination, not a count for individual informative sites.