Talk:20.109(S13):Phylogenetic analysis (Day7)

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Revision as of 12:47, 7 March 2013

Contents

General notes

I believe some groups are still in the process of reverse complementing inserts in the non-usual orientation.

Agi is in the process of trimming and analyzing four additional #709 clones prepped and sequenced yesterday.

T/R microbiome

Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].

Team Color Team Member Gull ID Sequence 1 (txt) Sequence 2 (txt) Sequence 3 (txt) Sequence 4 (txt) Sequence 5 (txt) Sequence 6 (txt) Sequence 7 (txt) Sequence 8 (txt) Species overview (xlsx) Alignment (mas) Tree (pdf)
Red Nick 702 Media:TR-Red_702-C1.txt Media:TR-Red_702-C2.txt Media:TR-Red_702-C3.txt Media:TR-Red_702-C7.txt Media:TR-Red_702-C8.txt Media:TR-Red-Species.xlsx Media:TR-Red-Blue-702.mas Media:TR-Blue-Red-tree.pdf
Red
Orange Daphne, Stas 712 Media:TR-Orange_712-C2.txt Media:TR-Org-712-C5.txt Media:TR-Org_712-C7.txt Media:TR-Org_712-C8.txt Media:TR-Orange_712.xlsx Media:TR-712-alignment.mas Media:TR-712-Alignment.pdf
Orange
Yellow Ebaa 664 Media: TR-Yellow_664-C1.txt Media: TR-Yellow_664-C4.txt Media: TR-Yellow_664-C8.txt Media: 664_S13-M1D7-template.xlsx Media: WFTR-664-Alignment.mas
Yellow Dominique 739 Media: TR-Yellow_739-C2.txt Media: TR-Yellow_739-C3_2.txt Media: TR-Yellow_739-C4.txt Media: TR-Yellow_739-C5.txt Media: TR-Yellow_739-C6.txt Media: TR-Yellow_739-C7.txt Media: TR-Yellow_739-C8.txt Media: 739_S13-M1D7-template.xlsx Alignment of all 739 from TR Media: TR-739-alignment.mas Tree of all 739 clones from TR Media:TR-739-tree.pdf Green Jesse 405 Media: TR-Green_405-C1.txt Media: TR-Green_405-C2.txt Media: TR-Green_405-C3-edit.txt Media: TR-Green_405-C4-edit.txt Media: TR-Green_405-C6-edit.txt Media: TR-Green_405-C7-edit.txt Media: TR-Green-405-Sepecies Overview.xlsx Media: WF-405_Alignment_with_TR_edited.mas Media: Phylogeny Tree TF and Steve only with edits to TR.pdf
Green
Blue
Blue Noa 702 Media:TR-Blue-702-C4.txt Media:TR-Blue-702-C5.txt Media:TR-Blue-702-C6.txt Media:TR-Blue-702-C8.txt Media:TR-Blue-702.xlsx Media:TR-Red-Blue-702.mas Media:TR-Blue-Red-tree.pdf
Pink Justin & Arturo 709 Media:TR-Pink_709-C5B.txt Media:TR-Pink_709-C6B.docx Media:TR-Pink_709B.xlsx
Pink 709 Media: B1.txt
Purple Sarah 739 Media:TR-Purple_739-C1.txt Media:TR-Purple_739-C2.txt Media:TR-Purple_739-C3.txt Media:TR-Purple_739-C4.txt Media:TR-Purple_739-C7.txt Media:TR-Purple_739-C8.txt Media:S13-M1D7-template-Sarah Yu.xlsx Media:module1.mas
Purple Mitali 664 Media:TR-Purple_664-C2.txt Media:TR-Purple_664-C5.txt Media:TR-Purple_664-C7.txt Media:TR-Purple_664-C8.txt Media:TR-Purple_664-MK.xlsx Media: WFTR-664-Alignment.mas
Platinum Emily 732 Media:TR_platinum_732_c2.txt Media:TR_platinum_732_c3.txt Media:TR_platinum_732_c4.txt Media:TR_platinum_732_c5.txt Media:TR_platinum_732.xlsx Media:emily and nikki m5 data.mas
Platinum Katie 405 Updated AGA start: Media:TR_Platinum_405_c1_edited.txt - Media:TR_Platinum_405_c3.txt - Media:TR_Platinum_405_c5.txt Media:TR_Platinum_405_c6.txt - Updated AGA start: Media:TR_Platinum_405_c8_edited.txt Media:KB_TR_Platinum.xlsx Katie before combining with Jesse: Media:KatieJesseSession.mas, Katie and Jesse (405) Aligned: Media: TR-405 alignment.mas, Katie, Jesse and Steve C. alignment: Media: WF-405 Alignment with TR edited.mas Katie and Jesse (405) finished tree - Media: TR-405-PhyloTree.pdf, Katie,Jesse Steve corrected tree (waiting on 4th 405 sample)- Media: 405 Phylogeny Tree TF and Steve only with edits to TR.pdf



W/F microbiome

Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].

Team Color Team Member Gull ID Sequence 1 (txt) Sequence 2 (txt) Sequence 3 (txt) Sequence 4 (txt) Sequence 5 (txt) Sequence 6 (txt) Sequence 7 (txt) Sequence 8 (txt) Species overview (xlsx) Alignment (mas) Tree (pdf)
Red Divya Arcot 702 Media: Divya_WF_Red_-_Insert_4,12.rtf‎ Media: WF_RED_-_Insert_5-13.rtf‎ Media: WF_RED_-_Insert_6-14.rtf‎ Media: WF_RED_-_Insert_7-15.rtf‎
Red Maria Escobar 702
Orange
Orange Katie Gorick 712 Media: WF-Orange_712-C3.txt Media: WF-Orange_712-C4.txt Media: WF-Orange_712-C6.txt Media: WF-Orange_712-C8.txt Media: WF-Orange_712.xlsx Media: REVISED WF-712 Alignment(WF_Orange+WF_Blue+TR_Orange).mas Media: REVISED WF-712 PhyloTree (TR-Orange + WF-Orange, Blue).pdf
Yellow Jenny Wei 739 Media: WF-Yellow_739-C1.txt Media: WF-Yellow_739-C3.txt Media: WF-Yellow_739-C4.txt Media: WF-Yellow_739-C5.txt Media: WF-Yellow_739-C7.txt Media: WF-Yellow_739-C8.txt Media: WF-Yellow_739.xlsx Media: WF-739-Alignment.mas Media: WF-739-Phylogenetic Tree.pdf
Yellow Karinna Vivanco 664 Media: WF-Yellow_664-C4.txt Media: WF-Yellow_664-C5.txt Media: WF-Yellow_664-C6.txt Media: WF-Yellow_664-C7.txt Media: WF-Yellow_664.xlsx WF-664-Alignment(+TR Purple).mas WF-664-Phylogenetic Tree(+TR Purple).pdf
Green Kevin Hu 732 Media: WF-Green_732-C4.txt Media: WF-Green_732-C5.txt Media: WF-Green_732-C7.txt Media: WF-Green_732.xlsx Media: WF-732 Alignment (TR-Platinum, WF-Green, Platinum).mas Media: WF-732-PhyloTree (TR-Platinum + WF-Green, Platinum).pdf
Green Steve Cho 405 Media: WF-Green_405-C1.txt Media: WF-Green_405-C3.txt Media: WF-Green_405-C7.txt Media: WF-Green_405.xlsx Media: WF-405 Alignment with TR edited.mas Media: 405 Phylogeny Tree TF and Steve only with edits to TR.pdf
Blue Emmanuel Carrodeguas 712 Media: WF-Blue_712-C1.txt Media: WF-Blue_712-C3.txt Media: WF-Blue_712-C4.txt Media: WF-Blue_712-C5.txt Media: WF-Blue_712-C7.txt Media: WF-Blue_712-C8.txt Media: WF-Blue_712.xlsx Media: WF-712-Alignment(WF_Blue+TR_Orange).mas Media: WF-712-Alignment(WF_Blue+TR_Orange).pdf
Blue Sachin Shinde 702 Media: WF-Blue_702-C7.txt Media: WF-Blue_702-C8.txt Media: WF-Blue_702.xlsx
Pink Alice Chen 712 Media: WF-Pink_712C4.txt Media: WF-Pink_712C5.txt Media: WF-Pink_712C6.txt Media: WF-Pink_712C7.txt Media: WF-Pink_712C8.txt Media: WF-Pink_712.xlsx
Pink Helen He 709 Media: WF-Pink_709-B1.txt Media: WF-Pink_709-B2.txt Media: WF-Pink_709-B3.txt Media: WF-Pink_709-B4.txt Media: WF-Pink_709-B6.txt Media: WF-Pink_709.xlsx Media: WF-709-Alignment.mas Media: WF-709-Alignment.pdf
Purple Jenny Van 664 Media: WF-Purple_664-C1.txt Media: WF-Purple_664-C2.txt Media: WF-Purple_664-C3.txt Media: WF-Purple_664-C4.txt Media: WF-Purple_664-C8.txt Media: WF-Purple_664.xlsx Media: WF-664-Alignment.mas
Purple
Platinum Eric Klinkhammer 732 Media: plt-1.txt Media: 2.txt Media: 3.txt Media: 4.txt Media: 5.txt Media: 6.txt Media: plt-7.txt Media: 8.txt Media: WF_732_sequence_data.xlsx Media: WF-732 Alignment (TR-Platinum, WF-Green, Platinum).mas Media: WF-732-PhyloTree (TR-Platinum + WF-Green, Platinum).pdf
Platinum

T/R microsporidia gels

Gel 1
Gel 1
Gel 2, bright
Gel 2, bright
Gel 3
Gel 3
Gel 4
Gel 4

Image:S13-M1D7-TR-Gel2-dim.jpg


W/F microsporidia gels

Gel 2
Gel 2
Gel 3
Gel 3
Gel 4
Gel 4
Gel 1, bright
Gel 1, bright
Gel 1, dim
Gel 1, dim


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