hyphy-analyses
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veg
HyPhy standalone analyses
Hi, I have encountered that the sequence order for the processed sequences differ from the original input fasta file. Is it possible to retain the order directly with pre-msa.bf? Thank...
Hello, I'd like to ask for some help with how best to use BUSTED-PH. I am trying to test whether selection is different between genes in species according to a...
Hi, I am trying to use the codon-msa pipeline to make my alignment more codon aware. I am encountering this issue when I run the pre-msa.bf it starts the analysis...
Good morning, I am working on a project to understand how a particular trait influences the number of genes under positive selection, at the level of the genome, and am...
fail to make
Hi, Thanks for developing this great tool! After successfully running `cmake ./`, I got the error when running `make -j MP` like below. I did not find a similar issue...
Dear Developer, Thank you very much for developing such a useful software, which has provided me with great help. But I have some doubts about how to interpret this result....
Hi @spond, I'm running the Relax scan analysis. It seems like I always have different results using the same dataset and command line, also on the example data. I wonder...
Hello, I I am running the pre-ma.bf script like so: hyphy hyphy-analyses/codon-msa/pre-msa.bf --input combined_seq.fasta I am running on a large memory node (1.5 Tb Memory) and get the following error:...
Hi I installed hyphy-analyses per the instructions like so: module load gcc openmpi git clone https://github.com/veg/hyphy.git hyphy-develop cd hyphy-develop git checkout develop cmake -DZLIB_LIBRARY="/global/scratch/users/nalexandre/miniconda3/lib/libz.a" -DZLIB_INCLUDE_DIR="/global/scratch/users/nalexandre/miniconda3/lib/" ./ make -j MP ./HYPHYMP...
Hello, I am having trouble getting the batch file for contrast-FEL to work on the command line. I'd like to include contrast-FEL in a workflow and would rather not use...