- Population genetics - dNdSpiNpiS dNdSpiNpiS -alignment_file=$pfas_file #if $cond_population.pop_select != "all_individuals": -population_file=$cond_population.pop_file #end if #if $cond_focal_species.source_select == "user_defined": -ingroup=$cond_focal_species.custom_name #else: -ingroup=$cond_focal_species.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 #if $cond_boot_opts.boot_opts_selector != "standard": -bs_replicates=$cond_boot_opts.bs_replicates -bs_sort=$cond_boot_opts.bs_sort -bs_confidence=$cond_boot_opts.bs_confidence #end if -gc_bin=$gc_bin -gapN_site=$gapN_site -gapN_seq=$gapN_seq -min_nb_codon=$min_codon -kappa=$kappa -remove_frameshift=$frameshift -compute_distances=$distance -tolerance_zone=$tolerance_zone -allow_internal_bc=$internal_bad_codons -print_header=$header -contig_usage=$contig_usage -out=dNdSpiNpiS_output -exec_mode=galaxy 1> $dNdSpiNpiS_log 2> $dNdSpiNpiS_error Use all focal individuals Use a custom population file Enter a custom species name Choose a species name in PopPhyl 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 Yes No tolerated forbidden Yes No Use all contigs Use even contigs only Use odd contigs only Use standard parameters Use custom parameters distance == "1" This program can be used to analyze all contigs of an alignment file in Fasta/PseudoFasta format. ---- List of analysis for the ingroup species: - Polymorphism analysis (piN, piS) - GC3 - Individual Heterozygosity - Fit - Weir and Cockerham (Evolution 1984) Fit - Non Oriented GC Analysis - Distance between individuals ---- Additionnal analysis when two species are defined: - Collect various indicators of Selection (nN, nS, fixN, fixS, etc.) - McDonald-Kreitman analysis