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. Update: even later than that. I can do the final addition to an existing #709 .mas file if need be, also including samples from a student who has been ill.
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.
T/R microbiome
Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].
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
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
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
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
Media: WF-712-Alignment(WF_Blue+TR_Orange+WF_Pink).mas
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