I am undertaking a project aiming to identify genome-wide signals of balancing selection. In doing so I am using the program VariScan to analyse the amount of genetic polymorphism.

To use VariScan I have been suggested to use the .phylip alignment file type. I currently have my data in .sam and .bam file types.

I haven't been able to find any ways of converting .bam to .phylip (apart from a module called bioscripts.convert, but my university analyses servers don't have this module). Are there any intermediary file types I have to convert .bam into first? Or are there ways to directly convert .bam file to .phylip.

Thank you for taking the time to read. Miles