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 Minou,

ReconstructAncestors returns a DataSet which has a very minimal printing functionality. Without getting into the details of HyPhy batch language, I would suggest that you first give Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login a try; one of the analyses implemented on the site is ancestral state reconstruction (ASR).

Let me know if this helps. If you need to implement ReconstructAncestors in a pipeline, I'll send you relevant code fragments.

Cheers,
Sergei

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

Hi Minou,

Have you tried going through the GUI? Follow the steps of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login (you can load binary 0-1 data), and when you have fitted the model, try 'Data->Ancestrors' menu.

Cheers,
Sergei