- Generate spectrums - Site_frequency_spectra Site_frequency_spectra -alignment_file=$pfas_file #if $cond_focal_species.focal_select == "user_defined": -ingroup=$cond_focal_species.focal_custom_name #else: -ingroup=$cond_focal_species.focal_dropdown_list #end if #if $cond_out_species.out_select != "no_outgroup" #if $cond_out_species.out_select == "user_defined": -outgroup=$cond_out_species.out_custom_name #else: -outgroup=$cond_out_species.out_dropdown_list #end if #end if -gapN_site=$gapN_site -gapN_seq=$gapN_seq -min_nb_codon=$min_codon -remove_frameshift=$frameshift -tolerance_zone=$tolerance_zone -allow_internal_bc=$internal_bad_codons -sample_size=$sample_size -kappa=$kappa -dfea_write_start=$dfea_start -dfea_min_NS_SNP=$dfea_min -exec_mode=galaxy 1> $SFS_log 2> $SFS_error Enter a custom focal species name Choose a species name in PopPhyl Focal Species List No (Analyze focal species only) Yes - Custom species name Yes - Choose a species name in PopPhyl Species List Remove frameshift-containing contigs Keep frameshift-containing contigs tolerated forbidden This program can be used to generate various site frequency spectrums from a multiple alignment file in Fasta/PseudoFasta format.