Talk:20.109(S14):Phylogenetic and primer analyses (Day7)

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Revision as of 18:45, 4 March 2014

Contents

General notes and updates

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)

T/R microbiota

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
Red
Orange CT-Q 312
Orange
Yellow
Yellow
Green CB 304 Media: TRGreen304C1.txt Media: TRGreen304C2.txt Media: TRGreen304C7R.txt Media: TRGreen304CB.xlsx Media: TR-304-Alignment.mas Media: TR-304-Tree.pdf
Green CR 304 Media: TRGreen304C11.txt Media: TRGreen304C12.txt Media: TRGreen304C13.txt Media: TRGreen304C14F.txt Media: TRGreen304C15.txt Media: TR_Green_304_C9-C15.xlsx Media: TR-304-Alignment.mas Media: TR-304-Tree.pdf
Blue KT 304 Media: TRBlue304C3.txt Media: TR-304-Alignment.mas Media: TR-304-Tree.pdf
Blue
Pink RCB 252 Media: TRPink252C1.txt Media: TRPink252C3.txt Media: TRPink252C5.txt Media: TR252Excel.xlsx
Pink HMH 252 Media: TRPink252C3B.txt Media: TRPink252C4B.txt



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

T/R microsporidia gels


W/F microsporidia gels


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