The Y DNA (STR) TMRCA calculator can now be accessed as a web application with full functionality here:
http://ehelix.pythonanywhere.com/
It is also embedded in this blog in a new page (above)
UPDATE (02/11/2014)
Another series of updates for the calculator:
To demonstrate the filtration utility, consider the YDNA E-V13 portion of the Bulgarian dataset from “Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry”, the *.csv file for this dataset can be downloaded from the link below as well :
http://ehelix.pythonanywhere.com/init/default/Example_Files.
When the file is uploaded, the application gives the option to analyze any subset of haplotypes with N>1 that is available, i.e in this case: Bulgaria/Central, Bulgaria/East and Bulgaria/West, in addition to all of the Haplotypes.
Picking each of the above subsets from the “Choose a filter” listbox and running them separately produces the following results:
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13
Sample size: 49
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--74.17 Generations(Modal)--74.17
Burgarella_Navascues--Generations(Median)--89.57 Generations(Modal)--89.57
Chandler--Generations(Median)--101.78 Generations(Modal)--101.78
Stafford--Generations(Median)--87.07 Generations(Modal)--87.07
Zhivotovsky--Generations(Median)--317.95 Generations(Modal)--317.95
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 2076 - 3358
Mean TMRCA: 2688
Median TMRCA: 2678
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13, Filter = Bulgaria/Central
Sample size: 17
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--50.30 Generations(Modal)--50.30
Burgarella_Navascues--Generations(Median)--61.98 Generations(Modal)--61.98
Chandler--Generations(Median)--64.37 Generations(Modal)--64.37
Stafford--Generations(Median)--53.36 Generations(Modal)--53.36
Zhivotovsky--Generations(Median)--245.10 Generations(Modal)--245.10
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 1408 - 2124
Mean TMRCA: 1753
Median TMRCA: 1748
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13, Filter = Bulgaria/East
Sample size: 16
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--85.28 Generations(Modal)--85.28
Burgarella_Navascues--Generations(Median)--100.69 Generations(Modal)--100.69
Chandler--Generations(Median)--116.98 Generations(Modal)--116.98
Stafford--Generations(Median)--102.94 Generations(Modal)--102.94
Zhivotovsky--Generations(Median)--339.67 Generations(Modal)--339.67
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 2387 - 3860
Mean TMRCA: 3094
Median TMRCA: 3078
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13, Filter = Bulgaria/West
Sample size: 16
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--88.42 Generations(Modal)--88.42
Burgarella_Navascues--Generations(Median)--107.76 Generations(Modal)--107.76
Chandler--Generations(Median)--126.34 Generations(Modal)--126.34
Stafford--Generations(Median)--107.00 Generations(Modal)--107.00
Zhivotovsky--Generations(Median)--373.64 Generations(Modal)--373.64
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 2475 - 4169
Mean TMRCA: 3275
Median TMRCA: 3274
Notice that if a filter is chosen, the applied filter's name will be appended to the Dataset field of the results with “Filter =”, if all haplotypes are requested on the other hand, the Dataset field will just contain the Dataset's name as specified by the user.
To double check if the ASD computation has been carried out correctly for the central TMRCA estimates, we can cross-check the result of the publication itself for the 3 regions (Table S7 in the supporting information), against the Zhivotvsky results computed by the app. (highlighted above) multiplied by 25 (for 25years/generation according to Zhivotovsky).
(Publication) app. Zhivotovsky results
Bulgaria/Central 6,100YA 6,127.5 YA
Bulgaria/East 8,400YA8,491.75 YA
Bulgaria/West 9,300YA9,341.00 YA
Close Enough!
See Also:
http://ethiohelix.blogspot.com/2012/06/finding-tmrca-of-ethiopian-ydna.html
http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html
http://ethiohelix.blogspot.com/2013/01/tmrca-calculations-from-plaster-nry.html
http://ethiohelix.blogspot.com/2013/02/the-zhivotovsky-multiplier.html
http://ethiohelix.blogspot.com/2013/03/african-sahel-ydna.html
http://ethiohelix.blogspot.com/2013/04/source-code-for-asd-based-tmrca.html
http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-j-lineages-in-ethiopian.html
http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-m13-lineages-in.html
http://ehelix.pythonanywhere.com/
It is also embedded in this blog in a new page (above)
UPDATE (02/11/2014)
Another series of updates for the calculator:
- User now able to utilize the previously idle first column in the csv file to group haplotypes together and thus compute the TMRCA for a specified group (see example below)
- The application now also accepts Locus names in NIST format as well.
- It also now automatically deletes any haplotype with a non-integer value given for any locus in the *.csv file. (instead of producing an error for that scenario)
To demonstrate the filtration utility, consider the YDNA E-V13 portion of the Bulgarian dataset from “Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry”, the *.csv file for this dataset can be downloaded from the link below as well :
http://ehelix.pythonanywhere.com/init/default/Example_Files.
When the file is uploaded, the application gives the option to analyze any subset of haplotypes with N>1 that is available, i.e in this case: Bulgaria/Central, Bulgaria/East and Bulgaria/West, in addition to all of the Haplotypes.
Picking each of the above subsets from the “Choose a filter” listbox and running them separately produces the following results:
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13
Sample size: 49
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--74.17 Generations(Modal)--74.17
Burgarella_Navascues--Generations(Median)--89.57 Generations(Modal)--89.57
Chandler--Generations(Median)--101.78 Generations(Modal)--101.78
Stafford--Generations(Median)--87.07 Generations(Modal)--87.07
Zhivotovsky--Generations(Median)--317.95 Generations(Modal)--317.95
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 2076 - 3358
Mean TMRCA: 2688
Median TMRCA: 2678
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13, Filter = Bulgaria/Central
Sample size: 17
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--50.30 Generations(Modal)--50.30
Burgarella_Navascues--Generations(Median)--61.98 Generations(Modal)--61.98
Chandler--Generations(Median)--64.37 Generations(Modal)--64.37
Stafford--Generations(Median)--53.36 Generations(Modal)--53.36
Zhivotovsky--Generations(Median)--245.10 Generations(Modal)--245.10
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 1408 - 2124
Mean TMRCA: 1753
Median TMRCA: 1748
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13, Filter = Bulgaria/East
Sample size: 16
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--85.28 Generations(Modal)--85.28
Burgarella_Navascues--Generations(Median)--100.69 Generations(Modal)--100.69
Chandler--Generations(Median)--116.98 Generations(Modal)--116.98
Stafford--Generations(Median)--102.94 Generations(Modal)--102.94
Zhivotovsky--Generations(Median)--339.67 Generations(Modal)--339.67
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 2387 - 3860
Mean TMRCA: 3094
Median TMRCA: 3078
****************************************************************************************************
Active Y-str file: Bulgaria_EV13.csv
Active Markers file: Full_marker_list.txt
Dataset: Bulgaria_EV13, Filter = Bulgaria/West
Sample size: 16
****************************************************************************************************
*Marker Details*
8 requested markers included in analysis (41 excluded):-
Markers not found in the Dataset: ['458', '590', '578', '594', '450', '572', '557', '570', '454', '455', '456', '388', '490', '492', '641', '406s1', '472', '520', '426', '568', '449', '448', '438', '460', '442', '447', '565', '617', '436', '446', '487', '444', '481', '537', '640', '534', '576', '531', '511', '437', 'gatah4']
Markers used in Analysis: ['19', '393', '392', '391', '390', '439', '389-1', '389-2']
****************************************************************************************************
*Coalescent Details*
Ballantyne--Generations(Median)--88.42 Generations(Modal)--88.42
Burgarella_Navascues--Generations(Median)--107.76 Generations(Modal)--107.76
Chandler--Generations(Median)--126.34 Generations(Modal)--126.34
Stafford--Generations(Median)--107.00 Generations(Modal)--107.00
Zhivotovsky--Generations(Median)--373.64 Generations(Modal)--373.64
****************************************************************************************************
*Pedigree/Familial Rates Summary*
Years/Generation: 28 - 33
TMRCA Range: 2475 - 4169
Mean TMRCA: 3275
Median TMRCA: 3274
Notice that if a filter is chosen, the applied filter's name will be appended to the Dataset field of the results with “Filter =”, if all haplotypes are requested on the other hand, the Dataset field will just contain the Dataset's name as specified by the user.
To double check if the ASD computation has been carried out correctly for the central TMRCA estimates, we can cross-check the result of the publication itself for the 3 regions (Table S7 in the supporting information), against the Zhivotvsky results computed by the app. (highlighted above) multiplied by 25 (for 25years/generation according to Zhivotovsky).
(Publication) app. Zhivotovsky results
Bulgaria/Central 6,100YA 6,127.5 YA
Bulgaria/East 8,400YA8,491.75 YA
Bulgaria/West 9,300YA9,341.00 YA
Close Enough!
See Also:
http://ethiohelix.blogspot.com/2012/06/finding-tmrca-of-ethiopian-ydna.html
http://ethiohelix.blogspot.com/2012/11/extensive-doctoral-thesis-on-ethiopian.html
http://ethiohelix.blogspot.com/2013/01/tmrca-calculations-from-plaster-nry.html
http://ethiohelix.blogspot.com/2013/02/the-zhivotovsky-multiplier.html
http://ethiohelix.blogspot.com/2013/03/african-sahel-ydna.html
http://ethiohelix.blogspot.com/2013/04/source-code-for-asd-based-tmrca.html
http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-j-lineages-in-ethiopian.html
http://ethiohelix.blogspot.com/2013/05/analyzing-ydna-m13-lineages-in.html