format problem(.beagle.gz files)

Question

[Daier]

After I call SNP, I get the file with suffix beagle.gz . The file format that raxml software needs to input is .phy. How can I convert it so that I can successfully use raxml software to build phylogenetic tree.

[Arup Ghosh]

How are you calling the SNPs?

[Daier]

Hello! I use angsd software call SNP