Question: Software for counting mutations over a tree
0
gravatar for confusedious
3.6 years ago by
confusedious420
Australia
confusedious420 wrote:

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 • 1.5k views
ADD COMMENTlink modified 3.5 years ago by jhc2.9k • written 3.6 years ago by confusedious420
1
gravatar for confusedious
3.5 years ago by
confusedious420
Australia
confusedious420 wrote:

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

ADD COMMENTlink written 3.5 years ago by confusedious420
3
gravatar for jhc
3.5 years ago by
jhc2.9k
Spain
jhc2.9k wrote:

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

ADD COMMENTlink written 3.5 years ago by jhc2.9k
1
gravatar for Joseph Hughes
3.6 years ago by
Joseph Hughes2.8k
Scotland, UK
Joseph Hughes2.8k wrote:

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

ADD COMMENTlink written 3.6 years ago by Joseph Hughes2.8k

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.

ADD REPLYlink written 3.5 years ago by confusedious420
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