mtDNA Haplogroup Analysis

Time 2020-10-01 04:03:11

Web Name: mtDNA Haplogroup Analysis

WebSite: http://dna.jameslick.com

ID:65893

Keywords:

mtDNA,Haplogroup,Analysis,

Description:

Need more help?There is a discussion about mthap on eng.molgen.org. You can also email your questions to me at james.lick@jameslick.com. So that I can best help you, please include a copy of the complete mthap report and/or your mtDNA data file in your email.References/Acknowledgementsvan Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. http://www.PhyloTree.org. doi:10.1002/humu.20921Turner, Ann 2009. CRS Transition Transversion Lookup Table http://dnacousins.vizachero.com/The feedback from DNA-Forums, 23andMe Community and eng.molgen.org users and others has helped to improve mthap.Haplogroup Data Change HistoryData Version 17.0 (2016-02-18) - Data updated to PhyloTree Build 17.Data Version 16.0 (2014-02-19) - Data updated to PhyloTree Build 16.Data Version 15.0 (2012-09-30) - Data updated to PhyloTree Build 15.Data Version 14.0 (2012-04-05) - Data updated to PhyloTree Build 14. Previous builds reconverted with some format changes.Data Version 13.0 (2011-12-28) - Data updated to PhyloTree Build 13.Data Version 12.1 (2011-11-12) - Data updated to fix error in L2a1 haplogroups.Data Version 12.0 (2011-07-21) - Data updated to PhyloTree Build 12.Data Version 11.1 (2011-03-07) - Added some GenBank sequence anchors to resolve some problematic matches.Data Version 11.0 (2011-02-08) - Data updated to PhyloTree Build 11.Data Version 10.0 (2010-08-16) - Data updated to PhyloTree Build 10.Data Version 9.0 (2010-06-23) - Data updated to PhyloTree Build 9.Data Version 8.0 (2010-06-04) - Initial release based on PhyloTree Build 8.Program Change HistoryProgram Version 0.19a (2013-04-08) - Small bug fix to prevent some unsupported files being misinterpreted.Program Version 0.19 (2012-08-11) - Updated to handle genome build 37 based 23andMe raw data files.Program Version 0.18 (2012-04-30) - Updated to support PhyloTree Build 14. Determine tree root dynamically and remove various hard codings of rCRS haplogroup. Fixed handling and display of insertions longer than 9 bases. Make PhyloTree data more modular. Replaced DNA Forums link with new eng.molgen.org discussion link.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.Program Version 0.16 (2011-07-11) - A change in 0.15 caused a new problem with optional matching markers appearing in the Extras list and is now fixed. Haplogroup K1ö now displayed correctly. Can now handle coding-region-only sequences correctly.Program Version 0.15 (2011-03-07) - Fixed incorrect scoring with reversions where data has no-call or untested marker. Treat nucleotides BDHVN as ambiguous (no-call) instead of heteroplasmy. Fixed some full sequence alignment problems. Fixed bug where optional matching markers sometimes appear in the Extras list. Handle commas and leading zeros in rCRSdiff files.Program Version 0.14 (2011-02-11) - Fixed incorrect coloring of untested reversions. Fixed incorrect coloring of optional markers. Fixed incorrect coloring of deletions.Program Version 0.13 (2011-02-10) - Added color coding of markers in each potential match. Added marker path from rCRS to each potiential match. Added initial support for GeneBase sequences (probably incomplete). Tweaked report terminology to aid in comprehension. Various minor big fixes.Program Version 0.12 (2011-02-05) - General: Scoring method overhauled to be more tolerant of large numbers of miscalls. Full Sequences: Fixed alignment regression in 0.11. Better handling of 3107N convention. Added code to treat other "N" markers as no-call. 23andMe: Added code to handle flipped markers in some results. Refined marker exclusion lists, blacklist ranges, and exclusion handling. Added code to handle 8285- marker correctly. Prefer transitions to transversions for ambiguous results.Program Version 0.11 (2011-01-26) - Based on early 23andMe v3 test results, a list of 14 potentially incorrect markers are excluded if found.Program Version 0.10 (2010-10-15) - Bugfix: Only check 23andMe flaky markers when 23andMe format is used.Program Version 0.09 (2010-09-30) - Added support for ASN1 format.Program Version 0.08 (2010-09-29) - Added support for lower case sequences. Added support for Genbank Flat File Format.Program Version 0.07 (2010-09-07) - Added support for explicit "-" deletions in some FTDNA FASTA files. Added a more helpful error when Family Finder data is uploaded. Limited unknown line errors to maximum of 10. Better auto-detection of ranges tested for those near rCRS. Adjustment of alignment in some cases where 'correct' alignment conflicts with phylogeny.Program Version 0.06 (2010-09-04) - Added support for FASTA sequence files. Fixed incorrect counting of FASTA and rCRSdiff markers.Program Version 0.05 (2010-08-24) - Added support for "Differences to CRS" files and heteroplasmy. Made some improvements in the scoring algorithm. Added FAQ and split directions off onto separate pages. Moved how to read from report to FAQ.Program Version 0.04 (2010-08-16) - Added support for deCODEme raw data files.Program Version 0.03 (2010-06-11) - Fixed: Non-phylogenetic markers incorrectly scored as extras. Old raw data with unreliable markers detected, warning given and relevant markers removed. HVR1/CR/HVR2 ranges changed to use PhyloTree standard from FTDNA standard. Includes directions on how to read the report. Include percent of mtDNA tested. Various improvements in report format/readability.Program Version 0.02 (2010-06-07) - Fixed: Incorrect scores with reversions. Better diagnostics for upload failures. Output now in HTML.Program Version 0.01 (2010-06-04) - Initial release.

TAGS:mtDNA Haplogroup Analysis 

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