Hi,

I am a very new user of HyPhy, and I would like to perform an analysis which can reconstruct the ancestral states of a given set of sequences.
I wrote a batch file which consists of opening the alignment, assigning a tree topology and a substitution matrix, and builds and otpimizes the likelihood function. Then, I expected to get the states of each internal node by using the command ReconstructAncestors, but instead I get the following output:
    6 species:{Node1,Node2,Node3,Node7,Node9,Node12};
    Total Sites:1;
    Distinct Sites:1
Could you please help me to know what is ReconstructAncestors command doing exactly? and Is there a way in Hyphy to make appear the states of all the internal nodes?

Thanks

Hi Sergei,

Thanks for the very quick answer. I looked at the ASR implemented on datamonkey site, but I think it cannot help me a lot since it accepts only nucleotide characters as input data. Though, my sequences are made of 0 and1. It would be so great if you can send me some relevant code fragments which can output the states of each internal node.

Thanks