markers and phylogeny

[elizabethmcd]

In create-genome-phylogeny no list for "all". RAXML also errors with options

# different ribosomal markers for archaea/bacteria/all
bacteria_list = ['rpL14_bact','rpL15_bact','rpL16_bact','rpL18_bact','rpL22_bact','rpL24_bact','rpL2_bact','rpL3_bact','rpL4_bact','rpL5_bact','rpL6_bact','rpS10_bact','rpS17_bact','rpS19_bact','rpS3_bact','rpS8_bact']
archaea_list = ['rpL14_arch','rpL15_arch','rpL16_arch','rpL18_arch','rpL22_arch','rpL24_arch','rpL2_arch','rpL3_arch','rpL4_arch','rpL5_arch','rpL6_arch', 'rpS10_arch','rpS17_arch','rpS19_arch','rpS3_arch','rpS8_arch']


if DOMAIN == 'archaea':    
    prot_list=archaea_list
elif DOMAIN == 'bacteria':
    prot_list=bacteria_list

[elizabethmcd]

Now remember why "all_list" was removed - this is not best practice, but this isn't reflected in the command-line options and documentation. Update code to remove "all" mention later downstream, and update documentation to give best practices of making separate archaea/bacteria trees and then concatenating afterwards if desired