Looking through this www.L257.org web site, it must be clear, this site was created with a specific idea in mind. There are sections that are set with a white background and other sections set with a light yellow background and these are very different. The white sections are in general text and comments. The formal yellow sections are all generated by a set of programs we developed for use in the project and highly simplify all sorts of daily tasks in Genetic Genealogy, such as e.g. finding matches between profiles, generating geographical maps, generating result sheets, etc. Most of these programs have been used for years creating this web site.
Central component of our set of software is a Y-Tree Database, that contains various versions of the Y-Tree of haplogroup R-Z18 and of other branches of Hg R. These trees are defined in terms of SNPs and the Y-Tree Database thus contains the key info on all SNPs. One could also call it a SNP Database, but as the key role of the database is to handle trees, the most appropriate name is Y-Tree Database.
The word "database" means a lot of different things to a lot of different people. We in the R-Z18 Project tend to see the database as a collection of data with a set of rules that describe the logical structure and meaning of that data, based on a well-defined terminology, together called the Data Model by most. The total (data + schema) is kept in a piece of software, called a database server. For the Y-Tree Database an open source database server called MySQL (pronounced MySequel) is used, but we use an complementary set of database tools as well, such as query tools, a graphic schema workbench and report generator.
The database provides a uniform interface for our software to access SNP and Y-Tree data and most of our programs use the Y-Tree Database in one form or another. The most recent example, and the program we are currently working on, combines all SNP test results from (1) FT-DNA; (2) YSeq; (3) Big-Y; and (4) Chromo-2 in a single overview. This task requires combining results of different labs that all test the same SNPs, but unfortunately often under different names. All these alternative names are in our Y-Tree Database and our software is therefore able to disentangle this interesting mess and will produce a clear report with the Terminal SNP for each profile in seconds for any haplogroup for which we have a tree.
One other function of our software tools is to generate tree diagrams for branches of the Y-Tree. We can generate a tree diagram for haplogroups other than R-Z18, by first importing the data into the database using a specifically designed bulk-load facility and then generating the diagram from the database. On the right is an example of this approach for the Y-Tree Backbone (this example required some manual tweaks as the tree apparently is in flux and we had to make a few interpretations and simplifications; see below). This is a static preview (snapshot of the "live" version). The live version allows to click on every underlined identifier: on a haplogroup (to get the subtree one level lower) and on a SNP (to go to the SNP Details Window) and offers a SNP Search Window (again to go to the SNP Details Window for any SNP).
|Level||Name (diagram)||Name (new)||SNP|
|13/14||NO/NO1 (combined)||K2a||M2335/F549/S22380, M214/Page39|
|14/15||P/P1 (combined)||K2b2 / K2b2a||P295/PF5866/S8, M45/PF5962|
Please note, there are other naming schemes such as this in use as well, in this schemea e.g. P1 is called QR, NO is called Hg X and NO1 in turn gets called NO. These changes do not alter much to the tree as such. And please note the diagram and the table are an approximation, in that (1) Hg NO and Hg NO1 have been kept together; (2) the same applies to Hg P and Hg P1; and (3) under Hg MS (K2b1) there are a few new groups that have been left out. These simplifications have been made to keep the complexity of the diagram in balance with the importance of the missing groups; the diagram is intended to give an overview and as such it will be useful. All of this leads to a formal (!!) designation of Haplogroup R = K2b2a2 (if you are in R, then try to work out during a rainy Sunday afternoon what your new Haplogroup designation under Hg K is going to be).