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

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