HyDe

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fileSegmentation fault (core dumping)

1

Hi This "fileSegmentation fault (core dumping)" occurred while running run_hyde.py. Is this because the input data exceeds the limit?

gyq-123

Segmentation fault -- empty lines error

1

Hi there, I keep receiving a segmentation fault error when trying to run HyDe. Are there limits to the size of the data matrix? For the life of me I...

cblair81

Can SNP data of only mutation sites be used as input data

1

HI, In the test file, the DNA sequence of species includig both variation and no variation sites was used as input data. Can only the SNP data of only variation...

syauwjl

confused results of gamma

1

Dear @pblischak , In your paper "HyDe: A python package for genome-scale Hybridization detection", it suggests that the gamma is the probabilities of P2.  However, in your source code,...

sandyplus

Gamma values > 1.0 and negative Z scores

2

Hello, I have concatenated a Rad dataset for 100 individuals between two populations with an outgroup for >200,000 bps (not just snps). I placed all individuals with ancestral coefficients from...

burbrink

Input need to filter minor allele frequence SNP?

1

Dear @pblischak , Is it necessary to filter SNPs with minor allele frequency (MAF) < 0.05? I want to make input from VCF. I wonder whether the MAF SNP will...

sandyplus

Phased data

5

Hello Paul, Can the input alignment be phased, or should it be the consensus with one line per individual? Thanks, Kyle

kyleaoconnell22

Graphical User Interface Beta Testers

1

I've been working on a v1.0 release of HyDe that cleans up and reorganizes the code and moves support over to Python 3.6+ only. The visualization module is being removed...

pblischak

OverflowError: value too large to convert to int

2

Hi, I've successfully installed HyDe and run both the test data, along with some test data of my own (5Kb sequences of the whole genome data below). Now, I'm trying...

ethering