[OPTIONS]
Compiled File=mega.chm
Title=MEGA 4 Help
Contents File=mega.hhc
Index File=mega.hhk
Default topic=RH_Copyright.htm
Default Window=main
Error log file=
Display compile progress=No
Display compile notes=Yes
Full-text search=Yes
Binary Index=No
Auto Index=No
Enhanced decompilation=No
Binary TOC=No
Flat=No

Full text search stop list file=C:\src\MEGA4\Help\HtmlHelp\System.stp
[WINDOWS]
main="","mega.hhc","mega.hhk","RH_Copyright.htm","",,,,,0x40000520,0,0x3006,[133,0,901,1024],0x0,0x0,,0,0,0
Second="",,,"","",,,,,0x40000020,0,0x1006,[584,102,994,972],0x0,0x0,,1,0,0

[TEXT POPUPS]

[MAP]
#include <HelpFile.hh>
#include <AlnBuilder_HC.hh>
#include <CentralDialogBox_HC.hh>
#include <ContextHelp_HC.hh>
#include <DataExplorerHelp_HC.hh>
#include <DistanceMethods_HC.hh>
#include <ErrorMessages_HC.hh>
#include <TextEditorHelp_HC.hh>
#include <TreeExplorer_HC.hh>
#include <Walk_Through_MEGA.hh>
#include <CaptionExpert_HC.hh>
#include <popuprefs_RH.hh>
#include <BasicStatistics_RH.hh>
#include <InputData_RH.hh>
#include <PhylogeneticTrees_RH.hh>
#include <Introduction_RH.hh>
#include <Glossary_RH.hh>
#include <FAQs_RH.hh>

[ALIAS]
#include mega.ali

[FILES]
RH_Acknowledgements.htm
Part_I__Getting_Started\Installing_MEGA\RH_System_Requirements.htm
Part_I__Getting_Started\Installing_MEGA\RH_Installing_MEGA.htm
Part_I__Getting_Started\Installing_MEGA\RH_Uninstalling_MEGA.htm
Part_I__Getting_Started\Features___Support\RH_Technical_Support.htm
Part_I__Getting_Started\Features___Support\RH_Reporting_Bugs.htm
Part_I__Getting_Started\Features___Support\RH_Guide_to_notation.htm
RH_Disclaimer.htm
Part_I__Getting_Started\Features___Support\RH_Using_MEGA_in_the_Classroom.htm
RH_Copyright.htm
Preface.htm
Part_I__Getting_Started\Features___Support\MEGA_Feature_List.htm
Part_I__Getting_Started\Features___Support\Whats_New_in_Version_3_0.htm
MEGA_Software_Development_Team.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\RH_MEGA_Format.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\General_Conventions\RH_Common_Features.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\General_Conventions\RH_Key_Words.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\General_Conventions\RH_Rules_for_Taxa_Names.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\General_Conventions\RH_Rules_for_Title_Statement.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\General_Conventions\RH_Rules_for_Description_Statement.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\RH_General_Considerations_Sequence_Data_Format.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Distance_Input_Data\RH_General_Considerationss_Distance_Data_Formats.htm
Part_III___Input_Data_Types_and_File_Format\Visual_Tools_for_Data_Management\Data_Subset_Selection\RH_Editing_Distance_Data.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Tree_Input_Data\RH_Editing_Tree_Data.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\General_Conventions\RH_Rules_for_Format_Statement.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\RH_Keywords_for_Format_Statement_Sequence_data.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Distance_Input_Data\RH_Keywords_for_Format_Statement_Distance_data.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\RH_IUPAC_single_letter_codes.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\General_Conventions\RH_Writing_Comments.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\Defining_Genes_and_Domains\RH_Writing_Command_Statements_for_Defining_Genes_and_Domains.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\Defining_Groups\RH_Writing_Command_Statements_for_Defining_Groups_of_Taxa.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\Defining_Genes_and_Domains\RH_Keywords_for_Command_Statements_Genes_Domains.htm
Part_III___Input_Data_Types_and_File_Format\Genetic_Code_Tables\RH_Built_in_Genetic_Codes.htm
Part_III___Input_Data_Types_and_File_Format\Genetic_Code_Tables\RH_Adding_Modifying_Genetic_Code_Tables.htm
Part_III___Input_Data_Types_and_File_Format\Genetic_Code_Tables\RH_Computing_Statistical_Attributes_of_the_Genetic_Code.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\RH_Importing_Data_From_Other_Formats.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_IG_Format_Files.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_NBRF_Format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_XML_format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_PIR_Format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Convert_GCG_Format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_MSF_Format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_Nexus_Format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_FASTA_format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_PHYLIP_Format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_PHYLIP_Noninterleaved_Format.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\Format_Specific_Notes\RH_Converting_CLUSTAL_Format.htm
Part_II__Assembling_Data_for_Analysis\HC_Text_Editor.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_TE_New.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_TE_Save.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_TE_Open.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_TE_Save_As.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_TE_Print.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_TE_Exit.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Edit_Menu\HC_TE_Undo.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Edit_Menu\HC_TE_Cut.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Edit_Menu\HC_TE_Copy.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Edit_Menu\HC_TE_Paste.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Edit_Menu\HC_TE_Font.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Search_Menu\HC_TE_Find.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Search_Menu\HC_TE_Find_again.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\Search_Menu\HC_TE_Replace.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_Reopen_in_Text_Editor.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_Close_File_in_Text_Editor.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_Delete_in_Text_Editor.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_Select_All_in_Text_Editor.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_Go_to_Line.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_Show_Line_Numbers_in_Text_Editor.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Text_Editor\Using_Text_Editor\File_Menu\HC_Word_Wrap_in_Text_Editor.htm
Part_II__Assembling_Data_for_Analysis\Some_Text_Editor_Utilities\HC_Convert_to_Mega_Format_in_Text_Editor.htm
HC_Convert_to_MEGA_Format_Dialog_Box.htm
Part_II__Assembling_Data_for_Analysis\Some_Text_Editor_Utilities\HC_Format_Selected_Sequence.htm
Part_II__Assembling_Data_for_Analysis\Some_Text_Editor_Utilities\HC_Reverse_Complement.htm
Part_II__Assembling_Data_for_Analysis\Some_Text_Editor_Utilities\HC_Copy_Screenshot_to_Clipboard.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\HC_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Export_Data_in_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Translate_Untranslate_in_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Setup_Select_Genes_Domains_in_Sequence_Data_Explorer_.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Select_Genetic_Code_Table_in_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Setup_Select_Taxa_Groups_in_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Quit_Data_Viewer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Show_Only_Selected_Sequences.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Use_Identical_Symbol.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Color_Cells.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Sort_Sequences.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Sort_Sequences_By_Sequence_Name.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Sort_Sequences_by_Group_Name.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Sort_Sequences_by_Group_and_Sequence_Names.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Sort_Sequences_As_per_Taxa_Group_Organizer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Restore_Input_Order.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Show_Sequence_Names.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Show_Group_Names.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Change_Font.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_Conserved_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_Variable_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_Parsimony_Informative_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_Singleton_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_0_fold_Degenerate_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_4_fold_Degenerate_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_2_fold_Degenerate_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Statistics_Menu\HC_Nucleotide_Composition.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Statistics_Menu\HC_Nucleotide_Pair_Frequencies.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Statistics_Menu\HC_Codon_Usage.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Statistics_Menu\HC_Amino_Acid_Composition.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Statistics_Menu\HC_Use_All_Selected_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Statistics_Menu\HC_Use_only_Highlighted_Sites.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Data_Menu_in_sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Display_Menu\HC_Display_Menu_in_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Highlight_Menu\HC_Highlight_Menu_in_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Statistics_Menu\HC_Stats_Menu_in_Sequence_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Visual_Tools_for_Data_Management\Data_Subset_Selection\HC_Selecting_Data_Subset_for_Sequence_Data.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Distance_Data_Explorer\HC_Dist_Exp_Options_dialog_box.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Distance_Data_Explorer\HC_Distance_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Distance_Data_Explorer\HC_Dist_Exp_File_Menu.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Distance_Data_Explorer\HC_Dist_Exp_Display_Menu.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Distance_Data_Explorer\HC_Dist_Exp_Average_Menu.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Distance_Matrix_Explorer\HC_Distance_Matrix_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Distance_Matrix_Explorer\HC_Dist_Matrix_Exp_Average_Menu.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Distance_Matrix_Explorer\HC_Dist_Matrix_Exp_Display_Menu.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Distance_Matrix_Explorer\HC_Dist_Matrix_Exp_File_Menu.htm
Part_IV___Evolutionary_Analysis\Computing_Basic_Statistical_Quantities_for_Sequence_Data\RH_Basic_Sequence_Statistics.htm
Part_IV___Evolutionary_Analysis\Computing_Basic_Statistical_Quantities_for_Sequence_Data\RH_Nucleotide_and_Amino_Acid_Compositions.htm
Glossary\RH_Nucleotide_Pair_Frequencies.htm
Glossary\RH_Codon_Usage.htm
Part_IV___Evolutionary_Analysis\Tests_of_Selection\Synonymous_Nonsynonymous_Tests\HC_Test_of_Selection_Tab.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Maximum_Parsimony__MP__Method\HC_MP_Analysis_Option_Dialog.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Specifying_Distance_Estimation_Options\HC_Dist_Analysis_Option_Dialog.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\NJ_UPGMA_Methods\HC_NJ_Analysis_Options.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Minimum_Evolution_Method\HC_ME_Analysis_Options.htm
Part_IV___Evolutionary_Analysis\Tests_of_Selection\Synonymous_Nonsynonymous_Tests\HC_Fisher_Exact_Test_Analysis_Options.htm
Part_IV___Evolutionary_Analysis\Tests_of_Selection\Synonymous_Nonsynonymous_Tests\HC_Z_test_Analysis_Options.htm
Part_IV___Evolutionary_Analysis\Tests_of_Selection\Synonymous_Nonsynonymous_Tests\HC_Disparity_Index_Analysis_Options.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Handling_Missing_Data_and_Alignment_Gaps\HC_Include_Sites_Option.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Specifying_Distance_Estimation_Options\HC_Distance_Model_Options.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\HC_Models_for_estimating_distances.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_No_of_differences_Nucleotide.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_p_distance_Nucleotide.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_Jukes_Cantor_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\HC_Jukes_Cantor_Gamma_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_Tajima_Nei_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\HC_Tajima_Nei_distance_Gamma_rates.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\HC_Tajima_Nei_Distance_Heterogeneous_patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\Gamma_Rates\HC_Tajima_Nei_Distance_Gamma_Rates_and_Heterogeneous_patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_Kimura_2_parameter_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\HC_Kimura_2_parameter_Gamma_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_Tamura_3_parameter_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\HC_Tamura_3_parameter_Gamma.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\HC_Tamura_3_parameter_Heterogeneous_patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\Gamma_Rates\HC_Tamura_3_parameter_Gamma_rates_and_Heterogeneous_patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_Tamura_Nei_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\HC_Tamura_Nei_distance_with_Gamma_model.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\HC_Tamura_Nei_distance_Heterogeneous_Patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\Gamma_Rates\HC_Tamura_Nei_distance_Gamma_rates_and_Heterogeneous_patterns_.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Synonymouse_and_Nonsynonymous_Substitution_Models\HC_Nei_Gojobori_Method.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Synonymouse_and_Nonsynonymous_Substitution_Models\HC_Modified_Nei_Gojobori_Method.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Synonymouse_and_Nonsynonymous_Substitution_Models\HC_Li_Wu_Luo_Method.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Synonymouse_and_Nonsynonymous_Substitution_Models\HC_Pamilo_Bianchi_Li_Method.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Synonymouse_and_Nonsynonymous_Substitution_Models\HC_Kumar_Comeron_Method.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\HC_No_of_differences_Amino_acids.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\HC_p_distance_Amino_acids.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\HC_Poisson_Correction_distance.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\Gamma_Distances\HC_Gamma_distance_Amino_acids.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Specifying_Distance_Estimation_Options\HC_bootstrap_method_to_compute_standard_error.htm
HC_Pseudorandom_number_generator.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\HC_Computing_the_Gamma_Parameter.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Handling_Missing_Data_and_Alignment_Gaps\RH_Alignment_Gaps_and_Sites_with_Missing_Information.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\HC_Dayhoff_Model.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\Gamma_Distances\HC_Dayhoff_and_JTT_distances_Gamma_rates.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\HC_Equal_Input_Model.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\HC_Equal_Input_Model_Gamma.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Amino_Acid_Substitution_Models\Heterogeneous_Patterns\HC_Equal_Input_Model_Heterogeneous_Patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\Gamma_Rates\HC_Equal_Input_Model_Gamma_rates_and_Heterogeneous_Patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\HC_MCL.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Gamma_Distances\Maximum_Composite_Likelihood_Gamma.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\Maximum_Composite_Likelihood_Heterogeneous_Patterns.htm
Part_IV___Evolutionary_Analysis\Computing_Evolutionary_Distances\Distance_Models\Nucleotide_Substitution_Models\Heterogeneous_Patterns\Gamma_Rates\Maximum_Composite_Likelihood_Gamma_Rates_and_Heterogeneous_Patterns.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\RH_Phylogenetic_Inference.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Phylogeny_Menu\Construct_Phylogeny\RH_UPGMA.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Phylogeny_Menu\Construct_Phylogeny\RH_Neighbor_Joining_Method.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Minimum_Evolution_Method\RH_Minimum_Evolution.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Phylogeny_Menu\Construct_Phylogeny\RH_Maximum_Parsimony_Method.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Maximum_Parsimony__MP__Method\RH_Alignment_Gaps_and_Sites_with_Missing_Information_Trees.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Statistical_Tests_of_a_Tree_Obtained\RH_Condensed_Trees.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Statistical_Tests_of_a_Tree_Obtained\RH_General_Comments_on_Statistical_Tests.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Tree_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Divergence_Time_Dialog_Box.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_File_Menu_in_Tree_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Image_Menu_in_Tree_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Subtree_in_Tree_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_View_Menu_in_Tree_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Compute_in_Tree_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Format_dialog_box_in_Tree_Explorer.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Tree_tab_in_Format_dialog_box.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Branch_tab_in_Format_dialog_box.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Taxon_Name_tab_in_Format_dialog_box.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Scale_Bar_tab_in_Format_dialog_box.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_TEx_Information_Box.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\HC_Subtree_Drawing_Options.htm
Part_V__Visualizing_and_Exploring_Data_and_Results\Tree_Explorer\Cutoff_Values_Tab_in_format_dialog_box.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\HC_Alignment_Builder.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Toolbars_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Data_Menu_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Edit_Menu_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Search_Menu_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Alignment_Menu_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Web_Menu_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Sequencer_Menu_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Menu_Items_in_the_Alignment_Explorer\HC_Display_Menu_in_Alignment_Explorer.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\CLUSTALW\HC_CLUSTALW_Options_DNA_Dialog.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\CLUSTALW\HC_CLUSTALW_Options_Protein_Dialog.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\Aligning_coding_sequences_via_protein_sequences.htm
Part_II__Assembling_Data_for_Analysis\HC_Web_Browser.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\BLAST\HC_About_BLAST.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\CLUSTALW\HC_CLUSTALW.htm
Part_II__Assembling_Data_for_Analysis\HC_Trace_Data_File_Viewer_Editor.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\HC_Introduction_to_Walk_Through_MEGA.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Constructing_Trees_from_Distance_Data.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Computing_Statistical_Quantities_for_Nucleotide_Sequences.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Estimating_Evolutionary_Distances_from_Nucleotide_Sequences.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Constructing_Trees_and_Selecting_OTUs_from_Nucleotide_Sequences.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Tests_of_the_Reliability_of_a_Tree_Obtained.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Test_of_Positive_Selection.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Creating_Multiple_Sequence_Alignments.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Working_With_Genes_and_Domains.htm
Part_I__Getting_Started\A_Walk_Through_MEGA\Managing_Taxa_With_Groups.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\HC_Main_MEGA_Window.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\File_Data\HC_File_Menu.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\File_Data\HC_Open_Data.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\File_Data\HC_Export_Data.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\File_Data\HC_Close_Data.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\File_Data\HC_Reopen_Data.htm
Part_III___Input_Data_Types_and_File_Format\Importing_Data_from_other_Formats\HC_Convert_To_MEGA_Format.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\File_Data\HC_Printer_Setup.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\File_Data\HC_Exit.htm
Part_III___Input_Data_Types_and_File_Format\Viewing_and_Exploring_Input_Data\Sequence_Data_Explorer\Data_Menu\HC_Data_Menu.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Data_Menu\HC_Data_Explorer.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\Defining_Groups\HC_Setup_Taxa_Groups.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\MEGA_Dialogs\HC_Setup_Taxa_Groups_Dlg.htm
Part_III___Input_Data_Types_and_File_Format\Visual_Tools_for_Data_Management\HC_Setup_Genes_Domains.htm
Part_III___Input_Data_Types_and_File_Format\Genetic_Code_Tables\HC_Select_Genetic_Code_Table.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Data_Menu\HC_Select_Preferences.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Data_Menu\HC_Handling_Gaps_and_Missing_Data.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Data_Menu\HC_Include_Codon_Positions.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Data_Menu\HC_Include_Labelled_Sites.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Choose_Model.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Distance_Menu.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Pairwise_Distances.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Overall_Mean.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Within_Group_Mean.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Between_Groups_Means.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Net_Between_Groups_Means.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Distances_Menu\HC_Sequence_Diversity.htm
Part_IV___Evolutionary_Analysis\Computing_Basic_Statistical_Quantities_for_Sequence_Data\HC_Pattern_Menu.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Phylogeny_Menu\HC_Phylogeny_Menu.htm
HC_Construct_Phylogeny.htm
HC_UPGMA.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Statistical_Tests_of_a_Tree_Obtained\Interior_Branch_Tests\HC_Neighbor_Joining.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Phylogeny_Menu\Construct_Phylogeny\HC_Minimum_Evolution.htm
HC_Maximum_Parsimony.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Phylogeny_Menu\HC_Display_Saved_Tree_Session.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Tree_Input_Data\HC_Display_Newick_Trees_from_File.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Statistical_Tests_of_a_Tree_Obtained\Bootstrap_Tests\HC_Bootstrap_Test_Phylogeny.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Statistical_Tests_of_a_Tree_Obtained\Interior_Branch_Tests\HC_Interior_Branch_Test.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Phylogeny_Menu\Relative_Rate_Tests\HC_Relative_Rate_Tests.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Molecular_Clock_Tests\HC_Tajima_Test_Relative_Rate.htm
HC_Selection_Menu.htm
Part_IV___Evolutionary_Analysis\Tests_of_Selection\Other_Tests\HC_Tajima_Test_of_Neutrality.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Selection_Menu\HC_Fisher_Exact_Test_Of_Selection.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Selection_Menu\HC_Z_Test_of_Selection.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Alignment_Menu\HC_Alignment_Menu.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Alignment_Menu\HC_Alignment_Explorer_CLUSTAL.htm
Part_II__Assembling_Data_for_Analysis\Some_Text_Editor_Utilities\HC_Open_Saved_Alignment_Session.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Alignment_Menu\HC_Browse_Databanks.htm
Part_II__Assembling_Data_for_Analysis\Building_Sequence_Alignments\BLAST\HC_BLAST_Search.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Alignment_Menu\HC_Show_Web_Browser.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Alignment_Menu\HC_Edit_Sequencer_Files.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Help_Menu\HC_Help_Menu.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Help_Menu\HC_Index.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\Main_MEGA_Menus\Help_Menu\HC_About.htm
HC_Citing_MEGA_in_Publications.htm
HC_Select_Distance_Options_Dialog.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\MEGA_Dialogs\HC_Genes_Domains_Dialog.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\MEGA_Dialogs\HC_Select_Genetic_Code_Table_Dialog.htm
Part_III___Input_Data_Types_and_File_Format\Genetic_Code_Tables\HC_Code_table_editor.htm
Appendix_B__Main_Menu_Items_and_Dialogs_Reference\MEGA_Dialogs\HC_Input_Data_Format.htm
Appendix_A__Frequently_Asked_Questions\RH_Finding_number_of_sites_in_pairwise_comparisons.htm
Appendix_A__Frequently_Asked_Questions\RH_Writing_only_4_fold_degenerate_sites_to_an_output_file.htm
Appendix_A__Frequently_Asked_Questions\RH_Computing_statistics_on_only_highlighted_sites_in_Data_Explorer.htm
Appendix_A__Frequently_Asked_Questions\RH_get_more_information_about_the_codon_based_Z_test_for_selection.htm
Appendix_A__Frequently_Asked_Questions\RH_Menus_in_MEGA_are_so_short.htm
Appendix_C__Error_Messages\HC_Blank_Names_Are_Not_Permitted.htm
Appendix_C__Error_Messages\HC_Domains_Cannot_Overlap.htm
Appendix_C__Error_Messages\HC_Fisher_s_Exact_Test_Has_Failed.htm
Appendix_C__Error_Messages\HC_Gamma_Correction_Failed_Because_p_0_99.htm
Appendix_C__Error_Messages\HC_Gene_Names_Must_Be_Unique.htm
Appendix_C__Error_Messages\HC_Inapplicable_Computation_Requested.htm
Appendix_C__Error_Messages\HC_Incorrect_Command_Used.htm
Appendix_C__Error_Messages\HC_Invalid_special_symbol_in_molecular_sequences.htm
Appendix_C__Error_Messages\HC_Jukes_Cantor_Correction_Failed.htm
Appendix_C__Error_Messages\HC_Kimura_1980_Distance_Correction_Failed.htm
Appendix_C__Error_Messages\HC_Missing_data_or_invalid_distances_in_the_matrix.htm
Appendix_C__Error_Messages\HC_No_Common_Sites.htm
Appendix_C__Error_Messages\HC_Not_Enough_Groups_Selected.htm
Appendix_C__Error_Messages\HC_Not_Enough_Taxa_Selected.htm
Appendix_C__Error_Messages\HC_Not_Yet_Implemented.htm
Appendix_C__Error_Messages\HC_p_distance_is_found_to_be_1.htm
Appendix_C__Error_Messages\HC_Poisson_Correction_Failed_because_p_0_99.htm
Appendix_C__Error_Messages\HC_Tajima_Nei_Distance_Could_Not_Be_Computed.htm
Appendix_C__Error_Messages\HC_Tamura_1992_Correction_Could_Not_Be_Applied.htm
Appendix_C__Error_Messages\HC_Tamura_Nei_Distance_Could_Not_Be_Computed.htm
Appendix_C__Error_Messages\HC_LogDet_Distance_Could_Not_Be_Computed.htm
Appendix_C__Error_Messages\HC_Dayhoff_Distance_Could_Not_Be_Computed.htm
Appendix_C__Error_Messages\HC_Equal_Input_Correction_Failed.htm
Appendix_C__Error_Messages\HC_Unexpected_Error.htm
Appendix_C__Error_Messages\HC_User_Stopped_Computation.htm
Appendix_C__Error_Messages\HC_Data_File_Parsing_Error.htm
Glossary\RH_Alignment_Gaps.htm
Glossary\RH_Bifurcating_Tree.htm
Glossary\RH_Branch.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Maximum_Parsimony__MP__Method\RH_Branch_and_Bound_algorithm.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Maximum_Parsimony__MP__Method\Heuristic_Search\RH_Close_Neighbor_Interchange_CNI.htm
Glossary\RH_Codon.htm
Glossary\RH_Complete_Deletion_Option.htm
Glossary\RH_Compress_Uncompress.htm
Glossary\RH_Condensed_Tree.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Maximum_Parsimony__MP__Method\RH_Consensus_Tree.htm
Glossary\RH_Constant_Site.htm
Glossary\RH_Degeneracy.htm
Glossary\RH_Domains.htm
Glossary\RH_Exon.htm
Glossary\RH_Extant_Taxa.htm
Glossary\RH_Flip.htm
Glossary\RH_Format_command.htm
Glossary\RH_Gamma_parameter.htm
Glossary\RH_Gene.htm
Glossary\RH_Genetic_Codes.htm
Part_III___Input_Data_Types_and_File_Format\Visual_Tools_for_Data_Management\RH_Groups_of_taxa.htm
Glossary\RH_Indels.htm
Glossary\RH_Independent_Sites.htm
Glossary\RH_Inferred_Tree.htm
Glossary\RH_Intron.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\Labelling_Individual_Sites\RH_Labeled_Sites.htm
Glossary\RH_Max_mini_branch_and_bound_search.htm
Glossary\RH_Maximum_Parsimony_Principle.htm
Glossary\RH_Mid_point_rooting.htm
Part_IV___Evolutionary_Analysis\Constructing_Phylogenetic_Trees\Maximum_Parsimony__MP__Method\Heuristic_Search\RH_Min_mini_algorithm.htm
Glossary\RH_Monophyletic.htm
Glossary\RH_mRNA.htm
Glossary\RH_Node.htm
Glossary\RH_Nonsynonymous_change.htm
Glossary\RH_Orthologous_Genes.htm
Glossary\RH_Outgroup.htm
Glossary\RH_Pairwise_deletion_option.htm
Glossary\RH_Parsimony_informative_site.htm
Glossary\RH_Polypeptide.htm
Glossary\RH_Positive_selection.htm
Glossary\RH_Protein_parsimony.htm
Glossary\RH_Purifying_selection.htm
Glossary\RH_Purines.htm
Glossary\RH_Pyrimidines.htm
Glossary\RH_Random_addition_trees.htm
Glossary\RH_Rooted_Tree.htm
Glossary\RH_RSCU.htm
Glossary\RH_Singleton_Sites.htm
Part_III___Input_Data_Types_and_File_Format\MEGA_Input_Data_Formats\Sequence_Input_Data\Labelling_Individual_Sites\RH_Site_Label.htm
Glossary\RH_Statements_in_input_files.htm
Glossary\RH_Swap.htm
Glossary\RH_Synonymous_change.htm
Glossary\RH_Taxa.htm
Glossary\RH_Topological_distance.htm
Glossary\RH_Topology.htm
Glossary\RH_Transition.htm
Glossary\RH_Transition_Matrix.htm
Glossary\RH_Transition_Transversion_Ratio_R.htm
Glossary\RH_Translation.htm
Glossary\RH_Transversion.htm
Glossary\RH_Tree_length.htm
Glossary\RH_Unrooted_tree.htm
Glossary\RH_Variable_site.htm
Glossary\RH_OLS_branch_length_estimates.htm
Glossary\RH_NCBI.htm
Glossary\RH_ABI.htm
Glossary\RH_Staden.htm
Glossary\RH_ClustalW.htm
Glossary\RH_Newick_Format.htm
Glossary\RH_Composition_Distance.htm
Glossary\RH_Disparity_Index.htm
Glossary\RH_Alignment_session.htm
Glossary\Maximum_Composite_Likelihood.htm
References\Saitou_and_Nei_1987.htm
References\Jukes_and_Cantor_1969.htm
References\Tajima_1993.htm
References\Tajima_and_Nei_1984.htm
References\Kimura_1980.htm
References\Tamura_1992.htm
References\Tamura_and_Nei_1993.htm
References\Li_et_al_1985.htm
References\Nei_and_Gojobori_1986.htm
References\Pamilo_and_Bianchi_1993.htm
References\Tanaka_and_Nei_1989.htm
References\Nei_and_Jin_1989.htm
References\Nei_et_al_1976.htm
References\Dayhoff_1978.htm
References\Goldman_1993.htm
References\Tamura_1994.htm
Nei_1991.htm
References\Sharp_et_al_1986.htm
References\Tajima_1983.htm
References\Nei_1986.htm
References\Pamilo_and_Nei_1988.htm
References\Felsenstein_1988.htm
References\Felsenstein_1986.htm
References\Sneath_and_Sokal_1973.htm
References\Fitch_and_Margoliash_1967.htm
References\Felsenstein_1993.htm
References\Estabrook_et_al_1975.htm
References\Lake_1987.htm
References\Swofford_1993.htm
References\Tateno_et_al_1982.htm
References\Sourdis_and_Krimbas_1987.htm
References\Rzhetsky_and_Nei_1992.htm
References\Rzhetsky_and_Nei_1993.htm
References\Studier_and_Keppler_1988.htm
References\Maddison_and_Maddison_1992.htm
References\Fitch_1971.htm
References\Eck_and_Dayhoff_1966.htm
References\Sankoff_and_Cedergren_1983.htm
References\Felsenstein_1978.htm
References\Hendy_and_Penny_1989.htm
References\DeBry_1992.htm
References\Tateno_et_al_1994.htm
References\Sourdis_and_Nei_1988.htm
References\Hendy_and_Penny_1982.htm
References\Kishino_and_Hasegawa_1989.htm
References\Efron_1982.htm
References\Felsenstein_1985.htm
References\Penny_and_Hendy_1985.htm
References\Felsenstein_and_Kishino_1993.htm
References\Hillis_and_Bull_1993.htm
References\Nei_et_al_1985.htm
References\Hedges_et_al_1992.htm
References\Nei_and_Kumar_2000.htm
References\Press_et_al_1993.htm
References\Comeron_1995.htm
References\Dopazo_1994.htm
References\Kumar_et_al_1993.htm
References\Zhang_et_al_1998.htm
References\Zhang_et_al_1997.htm
References\Zhang_and_Gu_1998.htm
References\Swofford_1998.htm
References\Yang_1999.htm
References\Gu_and_Zhang_1997.htm
References\Hillis_et_al_1996.htm
References\Li_1997.htm
References\Page_and_Holmes_1998.htm
References\Nei_et_al_1998.htm
References\Takahashi_and_Nei_2000.htm
References\Li_1993.htm
References\Swofford_et_al_1996.htm
References\Tajima_1989.htm
References\Kumar_and_Gadagkar_2001.htm
References\Tamura_and_Kumar_2002.htm
References\RH_Dayhoff_1979.htm
References\RH_Jones_et_al_1992.htm
Tamura_et_al_2004.htm
References\Tamura_et_al_2007.htm
References\Takezaki_et_al_1995.htm
References\Tajima_and_Nei_1982.htm
References\Purdom_et_al_2000.htm
References\Zuckerkandl_and_Pauling_1965.htm
HC_Caption_Expert.htm
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