Thursday, April 23, 2009

ft2phy: Y-DNA STR to ATGC conversion

ft2phy

Y-DNA Short Tandem Repeats to ATGC conversion




The software program "ft2phy" has been posted to the HAM Country Tools area. If you've ever thought it daunting using "ft2dna" to run LAMARC, or draw trees with DNAPARS or PHYML, or if you'd like to see the "alpha" or transversion ratios for your Group, then "ft2phy" can make life a bit easier for you.



"ft2phy" can read several lines of STR data from Family Tree DNA, and use the same input format that Dean McGee's Utility does. So, if you have saved your Dean McGee Utility data into a file, then "ft2phy" can read your data file in order to produce the ATGC conversion.


ft2phy can read multiple lines of data (up to 600 lines), and it sends the output to separate data files for each marker. These files can be used in genetics programs that are compatible with the Phylip format. This version can handle up to 37 markers.




http://home.earthlink.net/%7Eodoniv/HamCountry/HAM_DNA_Project/Tools/FT2PHY.html





- Enjoy











Thursday, April 16, 2009

Y-DNA Project Grouping with Genetic Distance

"How To" create Y-DNA Project Groups
by using Genetic Distance

Or, How To Group Y-DNA by Genetic Distance using Dean McGee's Y-DNA Comparison Utility


There has been some discussion about "How To" create Y-DNA Project Groups, which does not appear to be a standard yet for Project Administrators. Nor is there any existing software that will do this for you automatically.


Family Tree DNA has an option to permit the Project Administrator to sort their Project into "Groups," but provides little or no guidance on "How To" do this, nor do they offer software to do this for you.



The PHYLIP package "Kitsch" program will sort the kits for you, but it would be up to you to the Project Administrator to do the "Grouping" by hand.



Grouping your DNA Project properly can add value to the DNA evidence by showing who is more closely related, and who is not. And, you can base this upon the DNA information. A valuable concept because sorting into groups can become more of a scientific procedure, as well as enhancing the analysis of that data.


DNA Grouping enables the use of DNA evidence as a tool which is independent of the usual
genealogy methods. What that delivers is either a clear joining or clear separation of families that are either related or not related genetically.


That means that you should be able to use Genetic Distance to verify whether or not lines are
related when normal genealogy records have been destroyed, or are otherwise not yet discovered.


You may have noticed that some Project Administrators don't appear to know what to do with Genetic Distance. That is usually obvious if they post a Genetic Distance table which looks "jumbled." Here's an example of a poorly structured Genetic Distance table, using a few selected kits from the HAM DNA Project:






[ click on image to enlarge ]


Notice that the colored cells are jumbled all over the
place. You can look up your own ID and match it with other kits, but it makes little to no sense for the entire Project. A table that looks like this does not tell you how the DNA Project should be sorted into groups. In fact, it doesn't resemble anything like grouping at all.


There's a simple way to remedy this, which should give an overview of the entire Project at a glance. The remedy would be to sort the Genetic Distance table. Once you know how to sort the Genetic Distance table, an overview of the table starts to make sense.








Here's an example of the same kits that were used above, but this time they are sorted:




[ click on image to enlarge ]



Notice that the colors are now grouped together. Similar groups are now be found along the diagonal. The table is more symmetrical, and the "colored" cells now follow a recognizable pattern.


Then, the question becomes, what is the easiest way to sort the Genetic Distance table?



The answer is, that there are several ways to do sort
by Genetic Distance, but the simplest method is to sort on one of the Genetic Distance columns, then sort on the sums.


The easiest way to do that is by using Dean McGee's Y-DNA Utility to create the table, then sort on the first column.



Notice that column #1 of the "jumbled" Genetic Distance table is given in no particular order:





[ click on image to enlarge ]






The Genetic Distance values vary widely, and distances that are similar are certainly not on the table next to each other.













Here's column #1 of the "sorted" Genetic Distance table:









[ click on image to enlarge]




Notice that the Genetic Distance shows a similar increase, and the kits that are similar are next to each other on the table. You can check your work by creating a new Genetic Distance table with Dean McGee's Utility, and taking a second look at the grouping.











You
might have noticed the flaw by doing this simple sort (from the "sorted" Genetic Distance table above). That would be the grouping of kits #44176 and 47412. It doesn't sort correctly because they tested with a different number of markers. A simple "spot check" of the sort can usually show which kits did not sort correctly.


So, sorting your DNA Project by Genetic Distance (on one column) may leave a few unresolved groupings. That's because this example is a rough example only. You can get a better grouping by sorting a second time on sums for each row on either side of the diagonal. (It is possible to do some basic math in order to compensate for the varying number of markers tested.)



The trickiest part of using diagonal sums is that these sums could change with each re-arrangement. So, it may take a few iterations to get a better sorted table.



Or, if you are familiar with using the PHYLIP software package, a tree created with the "Kitsch" program will do the sorting for you. You can then use the MEGA software program to "Arrange Data for Balanced Shape." Arrange your data in the order suggested by the phylogram, and use that sorted data in your next run of Dean McGee's Utility.



The next run of Dean McGee's Utility should deliver a Genetic Distance table which shows the grouping for the DNA Project with colored cells along the diagonal.



Dean McGee's Y-DNA Comparison Utility can be found at:


http://www.mymcgee.com



If you are interested in the mathematics behind the Fitch-Margoliash method, a good starting point would be Professor Felsenstein's documentation on the software program "Kitsch" regarding the Fitch-Margoliash method with Evolutionary Clock:


http://evolution.genetics.washington.edu/phylip.html


The Genetic Distance table for the HAM DNA Project can be found with the output from Dean McGee's Utility at:

http://home.earthlink.net/%7Eodoniv/HamCountry/HAM_DNA_Project/HAM_DNA_McGee_output.html







Monday, April 6, 2009

Keeping Y-Search Up to Date


To the HAM DNA Project Participants:

I had been looking at mapped locations of (existing) towns called "Ham" in England tonight, and noticed that there are some possibilities of matching the FTDNA numbers with the locations of these towns. (There are more than two dozen towns in Britain called "Ham," about six "Ham Hill" locations, about seven "Ham Green" locations, etc.)

The best way to match DNA locations is with Y-Search.

Now, FTDNA hopes for a push in Britain in the upcoming year, so it is becoming more important to keep our Y-Search information up to date.

I say that because there is one town called "Ham" about 10 miles from Crewkerne (near Illminster), and another town called "Ham" near London. As you may recall from the 2007 DNA video, our Group #1 roughly matches these two areas in Y-Search. Our Franklin County line may have some parallels to the town called "Ham" near Frome (or Wells), if you recall the blog article about Glastonbury ties, for example. Tony, of course, has ancestors that come from a town called "Ham" near Brent Knoll (not too far from Wedmore).

Other possible examples could be the town of Ham near Plymouth, which the HAM lines from Maine are researching. (It would help if the HAM lines from Maine were participating in the DNA Project.)

Or possibility, since our Group #2 is matching Worchestershire, that puts them closest to the town called "Ham" (north of Bristol). Or, if our Group #4 is matching County Kent, there is a small town in County Kent called "Ham" near Sandwich (no pun intended).

You can check these maps out at Streetmap: http://www.streetmap.co.uk/


When we start getting participants in Britain, we should be getting some interesting information.

So, it is important to keep your Y-Search information up to date so that we have accurate information about our matches. Please enter your information on your oldest known ancestor correctly. In my case, that would be William HAM from Virginia, since any further ancestor has not yet been positively identified to date.

It was in May, 2008 that FTDNA changed the Haplotype Groupings:

This affected the following existing groups:


R1b1c became R1b1b2

I1a became I1

I1b became I

I1c became I2b

E3b1a became E1b1b1


Back then, I understood that FTDNA would be changing the Y-Search haplotype groups for us. But when I checked my Y-Search ID tonight, my haplotype group had been changed from "I1a" to "Unknown."

I had to manually set my haplotype group at the Y-Search database. So, I would guess everybody will need to check their haplotype group out there. This should help us to identify matches from other vendors as well.

You can change it by logging into Y-Search at:

http://www.ysearch.org/

- select "Edit An Existing User" (that would be your ID)

and the "Haplogroup" is just below the area with the DYS values, under your "Last name"

If you have not yet submitted your information to Y-Search, then you can do that by visiting your personal web page at FTDNA.




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Wednesday, April 1, 2009

2009 April Free DVD Special


Book Order Special - Free DVD
with any order in April


For the month of April, 2009 we will be running a DVD special. Anybody that buys a book will also receive a free DVD of
the "HAM Counties of Origin" videos.


A graphical overview of HAM
surname counties of origin in England, Virginia, and North Carolina. Hi-lites the name and date of the first person with the HAM surname to appear in each county. These are DVD versions of the videos posted to You Tube on HAM Surname County Origins in England, Virginia, and North Carolina (with the exception that the video on Virginia has been updated).

The DVD version of the Virginia origins video now also includes
HAM surname origins in an additional 9 counties in Virginia (but are not included in the You Tube version). These are counties mentioned in the book "A Short History of the HAM Surname in Virginia & NC."




VA Counties on DVD that are not in the You Tube version:


Albemarle County
Elizabeth City County
Frederick County

Fluvanna County
Isle of Wight County
King & Queen County

Pittsylvania County

Rockingham County

Shenandoah County





Which brings to total video coverage of HAM surname origins to about 35 counties in Virginia, based upon
information from our book, "A Short History of the HAM Surname in Virginia & NC."


This DVD also includes and "Extras" area, which includes the video on "How To Read HAM DNA Phylograms" as
well as the "HAM Book Trailer" video.


So, order a book during the month of April and receive a free DVD.






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