DnaSP DNA Sequence Polymorphism Version: 6.12 July 4, 2018 Copyright © 2018 by Julio Rozas et al. & Universitat de Barcelona. All Rights Reserved. DnaSP v6. Documentation Table of contents Contents ........................................................................................................... 4 Introduction ...................................................................................................... 6 What DnaSP can do ....................................................................................... 6 System Requirements and Installation .............................................................. 7 File Menu / Input and Output .............................................................................. 9 Input Data Files Formats ............................................................................... 10 FASTA Format ......................................................................................... 11 MEGA Format .......................................................................................... 12 NBRF/PIR Format ..................................................................................... 13 NEXUS Format ......................................................................................... 13 PHYLIP Format ........................................................................................ 17 HapMap3 Phased Haplotypes Format .......................................................... 17 Arlequin File Format ................................................................................. 18 Multi-MSA Formats ................................................................................... 19 Multiple Data Files Analysis (Batch Mode) ........................................................ 21 Multi-MSA Data File Analysis (All Positions; RADseq data; Stacks/PyRAD files) ... 23 Polymorphism and Divergence .................................................................. 24 Multi-MSA Data File Analysis (SNP Positions; VCF filles) ................................... 28 Polymorphism and Divergence .................................................................. 28 Haplotype Frequency Data File Analysis (*.arp) ............................................... 32 Open Unphase/Genotype Data File ................................................................. 35 Unfold a FASTA File (Diploid Individuals) with Ambiguity Codes to... ................ 37 Convert a FASTA File with Ambiguity Codes to 'Ns' ........................................ 38 Output ........................................................................................................ 39 Display Menu ................................................................................................... 39 Graphs Window ........................................................................................... 41 UCSC Browser ............................................................................................. 42 Data Menu ...................................................................................................... 43 Gaps in Sliding Window ................................................................................ 44 Assign Coding Regions ................................................................................. 44 Assign Preferred / Unpreferred Codons Table ................................................. 46 Define Domain Sets ...................................................................................... 46 Remove Positions ........................................................................................ 46 Define Sequence Sets ................................................................................... 47 Include / Exclude Sequences ......................................................................... 47 Analysis Menu ................................................................................................. 49 Polymorphic Sites ........................................................................................ 49 Estimating Synonymous & Nonsynonymous Changes .................................. 49 DNA Polymorphism ..................................................................................... 50 Effective Population Size ........................................................................... 52 InDel (Insertion-Deletion) Polymorphism ........................................................ 53 DNA Divergence Between Populations ............................................................ 55 Conserved DNA Regions ............................................................................... 56 2 / 112 DnaSP v6. Documentation Polymorphism and Divergence ...................................................................... 58 Polymorphism and Divergence in Functional Regions ....................................... 60 Synonymous and Nonsynonymous Substitutions ............................................. 61 Codon Usage Bias ........................................................................................ 63 Preferred and Unpreferred Synonymous Substitutions ...................................... 64 Gene Conversion ......................................................................................... 66 Gene Flow and Genetic Differentiation ............................................................ 67 Linkage Disequilibrium ................................................................................. 69 Recombination ............................................................................................ 71 Population Size Changes ............................................................................... 72 Fu and Li's (and other) Tests ......................................................................... 73 Fu and Li's (and other) Tests with an Outgroup ............................................... 75 HKA, Hudson, Kreitman and Aguadé's Test ..................................................... 78 McDonald and Kreitman's Test ....................................................................... 79 Tajima's Test ............................................................................................... 83 Overview Menu ................................................................................................ 85 Polymorphism Data ...................................................................................... 85 Polymorphism/Divergence Data ..................................................................... 86 MultiDomain Analysis ................................................................................... 87 Generate Menu ................................................................................................ 89 Concatenated Data File ................................................................................. 89 Shuttle to: DNA Slider .................................................................................. 89 Filtered Positions Data File ............................................................................ 90 Polymorphic Sites File .................................................................................. 91 Haplotype Data File ...................................................................................... 91 Translate to Protein Data File ........................................................................ 92 Reverse Complement Data File ...................................................................... 93 Prepare Submission to EMBL/GenBank Databases ............................................ 93 Tools Menu ..................................................................................................... 94 Coalescent Simulations (1-locus | 1-pop model) .............................................. 94 Coalescent Simulations (n-loci | 1-pop model) ................................................ 98 Coalescent Simulations (DnaSP v5) .............................................................. 100 HKA test. Direct Mode ................................................................................. 102 Window & Help Menus .................................................................................... 104 More Information & Distribution & Copyright .................................................... 105 Citation ..................................................................................................... 105 Authors .................................................................................................... 105 Acknowledgements .................................................................................... 106 References ................................................................................................ 106 3 / 112 DnaSP v6. Documentation Contents DnaSP Version: 6.12 Help Contents July 4, 2018 Running DnaSP, press F1 to view the context-sensitive help. What DnaSP can do Introduction System requirements Input and Output Input Data Files (FASTA format; MEGA format; NBRF/PIR format; NEXUS format; PHYLIP format; HapMap3 Phased Haplotypes format; VCF format; Multi-MSA formats; Arlequin format) Multiple Data Files Analysis (Batch Mode) Multi-MSA Data File Analysis (All Sites) Multi-MSA Data File Analysis (SNP Positions) Haplotype Frequency Data File Analysis Open Unphase/Genotype Data Convert a FASTA File with Ambiguity Codes to 'Ns' Output UCSC Browser Data Data Menu Define Sequence Sets Define Domain Sets Filter / Remove Positions Include / Exclude Sequences Analysis Polymorphic