mthap: an mtdna haplogroup analysis tool

Any discussions regarding mt-DNA markers, results or questions.

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Sat Mar 17, 2012 5:44 am
********************************************************************************************

Please note the new URL for mthap: http://dna.jameslick.com/mthap/

********************************************************************************************

This is a continuation of the previous discussions on the dna-forums site. A new release of mthap came out just a few days before dna-forums fell into a black hole, so we'll start out with that:

Program Version 0.17 (2012-02-28) - Added advanced options screen to customize various parameters. Can select from all builds of PhyloTree, and data files now completely independent of code and html. Can derive FTDNA/Genographic's 22-snp panel results, old or new version. Can handle arbitrarily ordered sequences. Additions/modifications to PhyloTree can be disabled. Report page title now customized with identifier (by default based on file name). Can handle rCRSdiff without base. Long segments of deletion will be considered unsequenced. Improved handling of indels in W. Sequenced ranges can now be specified. Can use reported SNPs for Genographic Project results. Better handling of 8285- 23andMe SNP. Fixed minor HTML errors to make everything fully W3C validated.
Last edited by jlick on Mon Apr 30, 2012 10:09 am, edited 1 time in total.
User avatar
Posts: 14
Joined: Sun Apr 01, 2012 6:48 pm
PostPosted: Fri Apr 06, 2012 9:07 am
Thank you for continuing your work James and the possibility to discuss it here !
What you think about the new Behar, Oven et al. A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root ?
I think it includes some nice refinement, interesting time estimates, good figures and a very good proposal.
Image

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Fri Apr 06, 2012 9:51 am
I'll have to take a look at that. It sounds interesting.

By the way, I just noticed that phylotree build 14 just came out. I usually update mthap the same day that a new build is out, but right now I'm on vacation and it would be too painful to update with just my phone for net access. I have ssh on my phone, so it would be possible, but there's a good chance something would get screwed up. It'll get updated on Sunday or Monday.
User avatar
Posts: 14
Joined: Sun Apr 01, 2012 6:48 pm
PostPosted: Fri Apr 06, 2012 5:45 pm
Wish you a nice easter weekend. The update can wait. :)

Posts: 70
Joined: Wed Mar 14, 2012 7:43 pm
Location: Maine
YDNA:
R1b-M157.2 (under Z6
MtDNA:
J1c2g
PostPosted: Sun Apr 08, 2012 11:13 am
jlick wrote:I'll have to take a look at that. It sounds interesting.

By the way, I just noticed that phylotree build 14 just came out. I usually update mthap the same day that a new build is out, but right now I'm on vacation and it would be too painful to update with just my phone for net access. I have ssh on my phone, so it would be possible, but there's a good chance something would get screwed up. It'll get updated on Sunday or Monday.


Build 14 of Phylotree is a MASSIVE update, as it includes thousands of new FMS haplotypes recently submitted by FT-DNA (a while back FT-DNA asked FMS testees for permission to forward their results). Many (especially Western European) clades have numerous new terminal subclades due to these submission.

While your program is a Godsend, I can imagine it will likely take more than a "couple of days" to update it to this new build of Phylotree. In the interim, individuals can go to http://www.phylotree.org/tree/main.htm directly and search for their haplotype.
Y Haplogroup: R1b - U106 - L48 - Z8 - Z6 - M157.2 (private sub-clade of Z6). 111 markers tested, Palindromic markers tested
mt Haplogroup J1c2g Full Mitochondrial test with an additional (private) mutation at 9974T
YSearch & Mitosearch ID: 3HSPN

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Sun Apr 08, 2012 2:42 pm
Actually the updating part is mostly automated, so I could update it in less than 5 minutes. What takes time is doing the test runs to make sure something didn't break.

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Sun Apr 08, 2012 3:43 pm
Boy, I sure walked right into that one. Not only were there about 50% more sequences added, but the data format changed significantly, so it's not gonna happen today.

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Mon Apr 09, 2012 1:54 pm
There's a lot of changes needed for this new release, so it will be a couple more days yet.

Posts: 326
Joined: Thu Mar 15, 2012 1:14 am

YDNA:
R1b-Z12*
MtDNA:
I3b (FMS)
PostPosted: Mon Apr 09, 2012 5:35 pm
jlick wrote:There's a lot of changes needed for this new release, so it will be a couple more days yet.


No worries, James. A delayed but proven release is far preferable to a quick and bug-ridden one.
Use Profile/Edit Profile in User Control Panel to add your Y-DNA and mtDNA values.
User avatar
Posts: 14
Joined: Sun Apr 01, 2012 6:48 pm
PostPosted: Tue Apr 10, 2012 10:17 am
GTC wrote:
jlick wrote:Boy, I sure walked right into that one. Not only were there about 50% more sequences added, but the data format changed significantly, so it's not gonna happen today.
There's a lot of changes needed for this new release, so it will be a couple more days yet.

No worries, James. A delayed but proven release is far preferable to a quick and bug-ridden one.

Agree! And the release/update would be much more interesting with 50% more sequences added. I hope this is one of the major steps to a fine graded tree and the resolution will be enough for all major uses in the future. Look at this statement in Behar, Oven et al. (2012):
Approaching a Perfect Phylogeny
[...] First, an almost final level of resolution for a number of western Eurasian clades was achieved, and the nodes of ancestral and derived haplogroups are often differentiated by a single mutation.
As an examplary comparison of the resolution of haplogroup H4 before/after (with image) is included.
Next

Return to mtDNA Discussions

Who is online

Users browsing this forum: No registered users and 1 guest