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

General notes and updates

I've added five additional #709 sequences to the existing alignment file, and posted the final alignment file and tree.

A student who is recovering from illness may also post a few additional #712 sequences and an updated alignment and tree file this weekend. She will not delete the old file, since many of you are already using it, but will simply add hers as another option to use in your reports.

Consider doing a "watch" on this page so you know when it changes.

I'd also like to link my Excel species worksheet right here. You can see that I had a few interesting decisions to make, which perhaps could apply to some of you as well. I don't expect any more changes to the trees at this point, but perhaps for the revision you can revisit your choices. More specifically: (1) in some cases I had only partial sequence, so I made naming decisions at a higher taxonomic level; (2) in one case the top choice was misleading because it was a partial sequence; (3) One sequence was longer than usual, which took a bit of extra searching to process during the trimming stage, because there was so little sequence overlap.

AgiStachowiak 16:19, 8 March 2013 (EST)

Final sample-wide alignment files and trees

One representative from each sample-based group should post a .mas and .pdf file here when data are in final form. That way we'll all have quick access to the location sub-trees.

Sample #	Alignment file (.mas)	Tree file (.pdf)
702	Media: Final_702_Alignment.mas	Media: Final_702_PhyloTree.pdf
709	Media: 709-final-alignment.mas	Media: S13_709-final-tree.pdf
712	Media: Final_712_Alignment.mas	Media: Final_712_PhyloTree.pdf
716	No clones worked	No clones worked
405	Media: Final_405_Alignment.mas	Media: Final_405_PhyloTree.pdf
664	Media: Updated WFTR-664-alignment.mas	Media: New Updated WFTR-664-tree.pdf
732	Media: 732-FinalAlignment.mas	Media: 732-FinalTree.pdf
739	Media: FINAL-739MA-alignment.mas‎	Media: FINAL-739-Phylogenetic_Tree.pdf‎

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 (seq order corrected)	Media: Updated TR-Yellow_664-C1.txt			Media: Updated TR-Yellow_664-C4.txt				Media: Updated TR-Yellow_664-C8.txt	Media: 664_S13-M1D7-template.xlsx	Media: Updated WFTR-664-alignment.mas	Media: New Updated WFTR-664-tree.pdf
Yellow	Dominique	739 (everything should be in correct seq order)		Media: TR-Yellow_739-C2f.txt	Media: TR-Yellow_739-C3.txt	Media: TR-Yellow_739-C4f.txt	Media: TR-Yellow_739-C5f.txt	Media: TR-Yellow_739-C6f.txt	Media: TR-Yellow_739-C7.txt	Media: TR-Yellow_739-C8f.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 new version still w/ TR + Jenny's-WF Media:TR-(JW-WF)-739-alignmentedit.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 new version still w/ TR + Jenny's-WF Media:TR + (JW-WF)-739-treeedit.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	Nikki	732	Media: TR-Grn_732-C1.txt	Media: TR-Grn_732-C2.txt	Media: TR-Grn_732-C3.txt	Media: TR-Grn_732-C4.txt		Media: TR-Grn_732-C6.txt	Media: TR-Grn_732-C7.txt		Media: TR-Grn_732.xlsx	Confirmed AGA start Media: TR-732-Alignment.mas	Media: TR-732-Tree.pdf
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 more complete file in Dominique's box
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	Media: WFTR-664-tree.pdf
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: WF_RED_4,12.txt‎	Media: WF_RED_5,13.txt	Media: WF_RED_6,14.txt‎‎	Media: WF_RED_7,15.txt		Media: WF_RED_-_S13-M1D7-template.xlsx‎	Media: WF-Red,TR-Red-Blue-702.mas‎	Media: WF_Red,_TR_Red,Blue.pdf‎
Red	Maria Escobar	702	Media: WF_red_702_17.txt‎	Media: WF_red_702_18.txt‎		Media: WF_red_702_20.txt‎		Media: WF_red_702_22.txt‎	Media: WF_red_702_23.txt	Media: WF_red_702_24.txt‎	Media: WF-Red-702.xlsx‎	Media: WF-702-alignment(TR-Red,TR-Blu,WF-Red,WF-Blu).mas	Media: WF-702-tree(TR-Red,TR-Blu,WF-Red,WF-Blu).pdf
Orange	Amelia Mockett	709	Media: WF-Orange_709-C1.txt	Media: WF-Orange_709-C2.txt			Media: WF-Orange_709-C5.txt			Media: WF-Orange_709-C8.txt	Media: S13-M1D7-WF-Orange-Mockett.xlsx	Media: WF-709-alignment-org.mas	Media: FULL 709 PhyloTree (TR Pink, WF Pink + 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: FULL 712 Alignment(TR_Orange + WF_Blue, Orange, Pink).mas	Media: FULL 712 PhyloTree (TR_Orange + WF_Orange, Blue, Pink).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	Media: WFTR-664-Alignment.mas	Media: WRTF-664-tree.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	Media: WF-702-alignment(TR-Red,TR-Blu,WF-Red,WF-Blu).mas	Media: WF-702-tree(TR-Red,TR-Blu,WF-Red,WF-Blu).pdf
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	Media: WF-712-Alignment(WF_Blue+TR_Orange+WF_Pink).mas	Media: WF-712-Alignment(WF_Blue+TR_Orange+WF_Pink).pdf
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: WFTR-664-Alignment.mas	Media: WRTF-664-tree.pdf
Purple	Zeinab Aboud	739	Media: WF-Purple_739-c1.txt	Media: WF-Purple_739-C2.txt	Media: WF-Purple_739-C3.txt		Media: WF-Purple_739-C5.txt			Media: WF-Purple_739-C8.txt	Media: WF-Purple_739.xlsx	Media: FINAL-739MA-alignment.mas‎	Media: FINAL-739-Phylogenetic_Tree.pdf‎
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