Instructions

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Input submission form

  1. Choose the type of input data for the TMRCA analysis, CSV or FTDNA and click the "Submit" button.

  2. If the chosen data type successfully uploads, a button will show up below with the caption, "Process TMRCA for *Your_Filename*", click that button.

  3. Assign a minimum sample size requirement of each subset to be analyzed, or leave blank if all subsets are to be included.

  4. Choose a set of markers from the pre-defined marker list or upload your own marker list file**.

  5. Only if the check box is on will calculations be performed on an uploaded marker list.

  6. Click "Compute TMRCA" and review the results, or click on the link to downlowad the input data for Fluxus Network Software©,
    or just click on the link "Clear and Upload New Y-STR file" to restart the process with a new file.


CSV file data input

*A CSV Y-STR input data file should first be made in the same format as any of the Example files shown here , more specifically:

FTDNA type data input

*Up to 67 markers of FTDNA style Y-STR haplotypes, in this order, can be correctly processed for analysis provided that the following steps are met:

  1. Paste haplotype repeats that are tab separated, for instance, items copied from excel spreadsheets or from 'Y-DNA Classic Chart' tables of FTDNA projects. Space separated repeats are not accepted. When copying a set of Y-STR haplotypes, do not include the header with the locus names, simply just highlight the repeats and up to five columns of IDs and paste it into the text box. A minimum of one ID column is required.

  2. Specify the column where the repeat data starts. If 'Auto' is selected, the app will attempt to find the column itself, provided that at least 5 different haplotypes are provided, it is advisable however to manually submit the column at which the repeats start, as this step must be done correctly or analysis will either be erroneous or not be allowed to proceed.

  3. If the pasted haplotypes include repeats in multi marker format; (a-b) for DYS385, DYS459, YCAII, CDY, DYF395S1 ,DYS413 and (a-b-c-d) for DYS464, like the FTDNA project tables do, then the "Parse Multi-Copy Marker" check box needs to be checked. If multi marker locus have already been separated in the pasted text, then there is no need to check this box. Note here that only markers a,b,c and d of DYS464 will be parsed, if repeats exist for DYS464 e,f and g, they will be ignored. Conversely, if pasting text with the multi-marker repeats already parsed and with data that includes repeat values for markers 464 e,f and g, then completely delete those columns before proceeding.

  4. If you want to analyze a specific FTDNA marker panel then choose it here. If no choice is made then data for the default maximum number of markers (= 67) will be generated.

  5. Choose an ID column that the calculator will use for filtering the data during analysis, if no choice is made, then by default all available ID columns will be concatenated to use as a label for each haplotype, consequently, filtering will not be possible during analysis.

  6. Give the dataset a name, if no name is given by the user, then the name 'Generic_YSTR_Data' will be assigned to the dataset.

  7. Click on the Parse button to process the pasted data, if all goes fine, a link will appear entitled 'Review Generated File', which will display the formatted data that will be used to perform the TMRCA computations. It would be good practice to review this file before proceeding to the computations.


Sample Size Control

If there is more than one unique subset in the dataset, then TMRCA computations will be carried out on each unique subset simultaneously, summarized results will then be printed for each subset in a tabular format. A "Sample Size Threshold" can be assigned if the user wants to require a minimum sample size from each subset to be analyzed , if nothing is assigned in this field, then the application will use N = 2 as the minimum sample size.

Markers

Marker list files are simple text files (*.txt) with a single DYS number written per row, several examples of Marker text files can be found under
the Pre-Defined Markers section in the Materials & Methods page.


Results


Fluxus Network Diagrams

The application will automatically create the requisite input file for the Fluxus Network Software in *.ych format. Right clicking on the link "Download Fluxus input data" and selecting save data in the browser's menu will save the file 'fluxus_network.ych', this file can then be imported into the software to create median joining network diagrams. The input data uses the default weight of 10 and will match the filter column of the the YSTR file to the 'lineage' column of the attribute entry (read Fluxus Network user guide for more details)

Additional Notes : The application does not maintain an active database, all uploaded files, other than being kept briefly during a session
to accommodate analysis on the most recently uploaded dataset, are completely deleted on a routine basis. It is therefore recommended to
save the results somewhere else once each round of analysis has completed.

Input submission form

  1. Enter the total sequence length in units of 1 million (Mb) or 1 thousand (Kb) base pairs

  2. Enter the Years / Generation

  3. Choose Analysis Type

    • If you know the Average Branch Length, L, and want to calculate the TMRCA, then
      choose 'L to TMRCA' and input the Average Branch Length in SNPS.

    • If you know the TMRCA and want to calculate the Average Branch Length, L, or compute
      the TMRCA using other mutation rate sources, then choose 'TMRCA to L' and input
      the TMRCA in KYA and the corresponding rate source used to calculate it.

  4. Click Submit and review the results

Results

  • Results are given in a tabular format below the input submission form

    1. All TMRCAs are given in KYA (= X 1000 Years before the present)

    2. The lower and upper bound TMRCA results are based on the 95% CI, which were derived in the original/source substitution rate publications

    3. The source, as well as the central TMRCA estimate columns are sortable