J2-M172_spreadsheet
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J2-M172 spreadsheetRelated Docs/Links
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for output of Research Tree, etc.
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http://tree.j2-m172.info/J2-M172 Stats
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https://docs.google.com/spreadsheets/d/1Kfvde5gHQ0EVV9lLVnjMLgtyOgLJQPZdywqyu2-idSc/edit?usp=sharing
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Last greater phylogeny update: 2015-07 ChrisR (further validation of ISOGG branches, J2b)
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BLAST for sequence similarity
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Indications Tree editing:http://genome.ucsc.edu/cgi-bin/hgBlat
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be careful to link parent ID to correct branch ID
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be careful when inserting or deleting rowsPublic J2 NGS phylogeny analysis
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use "Find and replace" to change hierarchical nameshttps://docs.google.com/spreadsheets/d/1TwxLOk2lO6GFzaCPMp4vCQJ_leQ_GfaRi5GyLowzE-8/edit#gid=675739459
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hierarchical Haplogroup name is used for Simple Tree output and sorting: check for correctness
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used 2-3 SNP names should be the most known and available for sanger sequencing and in chip tests
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do not sort columns in different order
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Branch ID Legend: ? placement vs brother branches unavailable, * upstream placement uncertified, (Private/Single), [under research], underlined: available for but not certified by sanger sequencing
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always check Research Tree output after edits
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(supposedly) recurrent SNPs are not considered (anymore) to define terminal/private clades when no additional sample without the same Y-DNA ancestor in the last 5 generations was tested positive.
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Ask ChrisR for further help
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© CC-BY-SA J2-M172 Research Team Phylogenetics
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Chris Rottensteiner, Bonnie Schrack, Angela Cone, Kamel Al Gazzah
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Acknowledgment J2 Phylogenetics (Partnering)
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L24: Al Aburto, Ludmilla Ryabchenko; J2: Ted Kandell, J2a: JaG; J2b: Vince Tilroe, Roman Sychev (YFull);
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Acknowledgment Phylogenetics
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Thomas Krahn (YSEQ, YBrowse, etc.)
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Greg Magoon & Andy Grierson (1kG Ytree, SNP research leaders)
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Vadim Urasin et al (yfull.com/tree), Dmitry Adamov et al. 2015 (Age Estimates)
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Ray Banks, Alice Fairhurst (ISOGG Y-DNA Haplogroup Tree)
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Mannis van Oven (phylotree/Y)
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Chris Morley (Geno 2.0 Ytree)
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Dave Reynolds (SNP compendium)
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