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

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 -- looks as though only one will be good. I may not finish until after class today, circa 5 pm.

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 Alignment of TR+ (Jenny's-WF) 739 Media:TR-(JW-WF)-739-alignment.mas	Tree of all 739 clones from TR Media:TR-739-tree.pdf Tree of TR + (Jenny's-WF) 739 Media: TR+(JW-WF)-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
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	Shanthi Ravi	405		Media: WF-PLT_405-C2.txt	Media: WF-PLT_405-C3.txt	Media: WF-PLT_405-C4.txt	Media: WF-PLT_405-C5.txt		Media: WF-PLT_405-C7.txt	Media: WF-PLT_405-C8.txt	Media: WF-PLT_405.xlxs

T/R microsporidia gels

Gel 1

Gel 2, bright

Gel 3

Gel 4

Gel 2, dim -- not sure why image won't show

W/F microsporidia gels

Gel 2

Gel 3

Gel 4

Gel 1, bright

Gel 1, dim