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.
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
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
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
