Doubts about use and implementation

[dreyes17]

Hello,

I was looking the code for knowing how to use it and what implementation was used in MPI_implementation. First of all, I was surprised about watching a variable named sharedQ in the folder SMP_ListBased in files such as frameWork.c and oBnB.c that are not present in the SMP_QueueBasedSynchronous neither in the MPI_Implementation. From my comparisson of the code and accordingly to what was written in the paper I suppose that MPI_Implementation is the Queue one, but that variable was disturbing me.

Another question is about the input variables in the MPI_Implementation. The arrangements_per_level input paramenter is related to the number of arrangements of TBR for each level. The other tuning parameter mentioned in the paper (cardinality k of the set of subtrees that a processor receives from the shared queue) couldn't be inserted right? (In case it is the Queue method)

Finally, I have doubts regarding the input matrix (alignment). In the example file xac there are no N characters for undeciphered nucleotides nor gaps. This algorithm is able to handle both or some of them?

Thank you very much for sharing the code and the research!