Hi Dean, I apologize for the DYS389i and DYS389ii comment. I checked the ych file that your program produced and it had converted the value of DYS389ii. I think what threw me off was that the name of D3892 remained the same instead of being changed to something like D389B, which SMGF uses. Regarding the handling of missing markers, possibly it would be better to post a warning message when missing markers are encountered instead of displaying the ych file. Fluxus turned itself off when I tried to run a file with a lot of zeros in it. I had run a small sample file with no problem so I couldn't figure out what the problem was. I even posted a question on the Genealogy-DNA mailing list about this, but had no responses. Then I figured it must have been all the zeros, and it was. I don't know of an acceptable format for missing markers that Fluxus will accept. I did use your feature for disabling markers and it worked great, like everything else in your program. Thank you so much for developing this software for us would be genetic genealogists. I wish I could produce such nice looking HTML tables from Excel 97 using Microsoft's conversion program. Bruce Baird In a message dated 3/26/2006 7:12:34 PM Central Standard Time, hdmcgee000@comcast.net writes: Bruce, Yes, missing markers are a problem for making cladograms with the Y-Utility. The instructions indicate that the "haplotype data for all sets of results have the same number of markers". If you have a suggestion for a better way of handling missing markers, please let me know. Is there a format accepted by the Fluxus software that accounts for missing markers? The Y-Utility has been upgraded with the capability of enabling each marker. So, you can disable the markers which exist for only part of the set of results. Then the .ych file will only contain the values for enabled markers. Regarding DYS389i and DYS389ii, these are handled properly. The Y-Utility for your example would convert DYS389ii to the value of 17 and leave the values of 12 and 13 for DYS389i, so there would only be one mutation. The colors in the displayed tables also handle this marker properly, although the displayed value of DYS389ii is not changed. I would be interested in any suggestions for a better way to handle DYS464. Please let me know if the Y-Utility is not working properly in any way. -Dean McGee

Brian, Thank you for your comments. I have modified the utility to post a warning if there are any missing values in the set of enabled markers when Fluxus output is enabled. The warning recommends to either disable the offending markers or remove offending haplotypes. Also D3892 has been renamed to D389B. -Dean > From: Bbairdsr@aol.com [mailto:Bbairdsr@aol.com] > > Regarding the handling of missing markers, possibly it would > be better to > post a warning message when missing markers are encountered > instead of displaying > the ych file. Fluxus turned itself off when I tried to run a > file with a lot > of zeros in it. I had run a small sample file with no > problem so I couldn't > figure out what the problem was. I even posted a question on the > Genealogy-DNA mailing list about this, but had no responses. > Then I figured it must have > been all the zeros, and it was. I don't know of an > acceptable format for > missing markers that Fluxus will accept.