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Software for counting mutations over a tree

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?

phylogenetics
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updated by jhc jhc • written by confusedious confusedious

3 answers

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

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written by confusedious confusedious

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

enter image description here

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written by jhc jhc

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

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written by Joseph Hughes Joseph Hughes

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.

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written by confusedious confusedious

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