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

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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)

An updated version of the #739 alignment file & tree was posted to get rid of duplicates of some insert sequences.

Sarah N. Yu 21:13, 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-739-MA-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
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
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 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

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