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

T/R microbiota

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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	AK	308	Media:TRRed308C1		Media:TRRed308C3.txt	Media:TRRed308C4.txt		Media:TRRed308C6.txt		Media:TRRed308C8.txt	Media:TRRed308.xls
Red	LT	308		Media:TRRed308C2B.txt	Media:TRRed308C3B.txt	Media:TRRed308C4B.txt	Media:TRRed308C5B.txt	Media:TRRed308C6B.txt		Media:TRRed308C8B.txt	Media:TRRed308.xls
All	SKH	308		Media:TR308S2.txt	Media:TR308S3.txt	Media:TR308S4.txt					Media:TRRed308star.xlsx
Orange	CT-Q	312	Media:TROrange312C1.txt	Media:TROrange312C2.txt	Media:TROrange312C3.txt						Media:TROrange312.xlsx
Orange	AN	308		Media: TROrange308AC2.txt	Media: TROrange308AC3.txt	Media: TROrange308AC4.txt	Media: TROrange308AC5.txt				Media: TROrange308AC.xlsx
Yellow	REDO	312		Media: 312-2.txt	Media: 312-4.txt	Media: 312-5.txt	Media: 312-7.txt	Media: 312-10.txt			Media: 312-REDO-samples.xlsx
Yellow	SW	312	Media: TRYellow312C1b.txt	Media: TRYellow312C2.txt	Media: TRYellow312C2b.txt			Media: TRYellow312C6B.txt			Media: TRYellow312.xlsx
Green	CB	304	Media: TRGreen304C1.txt	Media: TRGreen304C2.txt					Media: TRGreen304C7R_R.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: TRGreen304CR.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	MG	252	(see Pink)									Media: TR-252-Aligment-partial.mas	Media: TR-252-Tree-partial.pdf
Pink	RCB	252	Media: TRPink252C1.txt		Media: TRPink252C3.txt		Media: TRPink252C5.txt				Media: TR252Excel.xlsx
Pink	HMH / MG	252			Media: TRPink252C3B.txt	Media: TRPink252C4B.txt	Media: TRPink252C5B.txt	Media: TRPink252C6B.txt

W/F microbiota

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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	TVK	286	Media:WFRed286C1.txt	Media:WFRed286C2.txt		Media:WFRed286C4.txt	Media:WFRed286C5.txt	Media:WFRed286C6.txt	Media:WFRed286C7.txt		Media:WFRed286_2.xlsx	Media:WF-286-alignment-partial.mas	Media:WF-286-Tree-partial.pdf
Red	JQX	286	Media:WFRed286C1B.txt	Media:WFRed286C2B.txt	Media:WFRed286C3B.txt	Media:WFRed286C4B.txt	Media:WFRed286C5B.txt	Media:WFRed286C6B.txt		Media:WFRed286C8B.txt	Media:WFRed286.xlsx
Orange	EAK	286	Media:WFOrange286C9.txt								Media:Orange286.xlsx
Orange
Yellow	TCD	294(1)	Media:WFYellow294(1)C1.txt	Media:WFYellow294(1)C2.txt	Media:WFYellow294(1)C3.txt‎ Short sequence	Early termination	Media:WFYellow294(1)C5.txt‎ Only used reverse sequence	Very poor quality -- can't read	Media:WFYellow294(1)C7.txt Only used reverse sequence	Media:WFYellow294(1)C8.txt Only used reverse sequence	Media:WFYellow294(1).xlsx
Yellow	HRS	294(2)	Media: WFYellow294(2)C1.txt	Media: WFYellow294(2)C2.txt	Media: WFYellow294(2)C3.txt	Media: WFYellow294(2)C4.txt Only use sequence from Reverse Primer	Media: WFYellow294(2)C5.txt	Media: WFYellow294(2)C6.txt	Media: WFYellow294(2)C7.txt	Media: WFYellow294(2)C8.txt Does not start with AGA	Media: WFYellow294(2).xlsx
Green	P^2	290	Media: WFGreen209C6.txt								Media: WFGreen290.xlsx
Green	IK	290								Media: WFGreen290C8.txt	Media: WFGreen290_2.xlsx	Media:WF-290-alignment-partial.mas	Media:WF-290-Tree-partial.pdf
Blue	VAM	290	Media:WFBlue290C1.txt	Media:WFBlue290C2.txt		Media:WFBlue290C4.txt				Media:WFBlue290C8.txt	Media:WFBlue290.xlsx
Blue	VT	274	Very short product	Media:WFBlue274C2.txt (Beginning and end of sequence is correct, middle of sequence is ambiguous due to early termination)	Media:WFBlue274C3.txt	No liquid culture growth	Media:WFBlue274C5.txt	Media:WFBlue274C6.txt	No priming	No priming	Media:WFBlue274.xlsx
Pink	MZ/GG	274	Media:WFPink274G1.ape.txt	Media:WFPink274G2.ape.txt	short sequence	Media:WFPink274G4.ape.txt	no priming	Media:WFPink274G6.ape.txt	poor quality	Media:WFPink274G8.ape.txt	Media:WFPinkSpecies.xlsx
Pink	GG/MZ	274	Media:WFPink274M1_shortRead.ape.txt	no priming	Media:WFPink274M3_shortRead.ape.txt	no priming	Media:WFPink274M5 short read.ape.txt	Media:WFPink274M6 short read.ape.txt	no priming	Media:WFPink274M8.ape.txt short read	no sequences long enough/usable to blast
Purple	KS	260			No priming	No priming	Media:WFPurple260C5B.txt	No priming		No priming	Media:WFPurple260worksheet.xlsx
Purple	AM	260		Short sequence			Media:WFPurple260C5.txt				Media:WFPurple260Overview.xlsx
Silver	MO	252		Media:WFSilver252C1.txt		Media:WFSilver252C3.txt		short reading	poor quality	Media:WFSilver252C8.txt	Media:WFSilver252.xlsx	Media:WFSilver252_alignment.mas	Media:WFSilver252_Tree.pdf
Silver	SW	252		Media:WFSilver252C1B.txt	Media:WFSilver252C2B.txt				Poor quality	Poor quality
White	JRI	260	Media:WFWhite260C1.txt	short sequence				Media:WFWhite260C6.txt‎	Media:WFWhite260C7.txt‎	Media: WFWhite260C8.txt	Media: WFWhite260.xlsx	Media: WF260alignment-partial.mas	Media: WF260Tree-partial.pdf
White	CTC	260						Media:WFWhite260C14.txt			Media:WFwhite260.xlsx	See above row

T/R microsporidia gels

Gel number	Reference samples	Group 1	Group 2	Picture
T/R 1	Specificity (VC, EH, mixture)	Orange	Yellow	Media:TR1.BMP
T/R 2	Specificity (VC, EH, mixture)	Blue	W/F Green	Media:TR2.BMP
T/R 3	Sensitivity (EH: lo, mid, hi)	Red	Green
T/R 4	Sensitivity (EH: lo, mid, hi)	Pink	Blue

W/F microsporidia gels

Gel number	Reference samples	Group 1	Group 2	Picture
W/F 1	Specificity (VC, EH, mixture)	Blue	Purple	Media:WF1.BMP
W/F 2	Specificity (VC, EH, mixture)	Silver	White	Media:WF2.BMP
W/F 3	Sensitivity (EH: lo, mid, hi)	Red	Orange
W/F 4	Sensitivity (EH: lo, mid, hi)	Yellow	Pink