Dear Nicolas,
Looks like you are running an old version of HyPhy (maybe). Also, you need to use explicit inputs (not numerical equivalents) when composing user-input redirection as in the example at the bottom of the message (this example assumes that you paste some rough tree into the alignment to estimate global model parameters from - this really speeds up the process). Also, since you are calling 'SequentialAddition' directly, you can skip the dialog options needed to select this analysis first.
HyPhy will understand absolute paths and also paths relative to the current batch file (not the binary).
As far as calling goes, try:
Code:$HYPHY BASEPATH=/absolute/path/to/HyPhy/ your/batch/file.bf
Finally, HyPhy is quite slow when it comes to phylogenetic inference (because it is a secondary feature), but you can infer trees with complex models (at least for small data sets). Also, many analyses will run in parallel on an MPI cluster if you have access to one.
Cheers,
Sergei
Code: RequireVersion ("0.9920060821");
stdinRedirect = {};
filePath = "/Users/sergei/HyPhy/data/hiv.aa";
stdinRedirect["00"] = "Nucleotide/Protein";
stdinRedirect["01"] = filePath;
stdinRedirect["02"] = "Given Order";
stdinRedirect["03"] = "No Constraint";
stdinRedirect["04"] = "Complete NNI";
stdinRedirect["05"] = "4";
stdinRedirect["06"] = "JONES+F";
stdinRedirect["08"] = "Rate Variation";
stdinRedirect["09"] = "Gamma";
stdinRedirect["10"] = "4";
stdinRedirect["11"] = "First Three";
stdinRedirect["12"] = "Get from a user tree";
stdinRedirect["13"] = "y";
batchFileToRun = HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "SequentialAddition.bf";
ExecuteAFile (batchFileToRun, stdinRedirect);