Talk:20.109(S15):Phylogentic analysis (Day8): Difference between revisions

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Line 1: Line 1:
==Upload alignment files here==
==Upload alignment files here==
'''All birds MEGA file + extra data from S14 (birds 312, 290, 274): [[media:S15data_all_v1.mas | MEGA file]]'''<br>
'''ID Files that correspond to MEGA file above: [[media:S15_IDFile_spaces.txt |ID file with spaces]] <br>  [[media:S15_IDFile_nospaces.txt |ID file without spaces]] '''


Name your alignment file according to this example: WF-TeamColor-alignment-FINAL
Name your alignment file according to this example: WF-TeamColor-alignment-FINAL
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|-
|-
|Orange
|Orange
|
|[[media:TROrange302.mas|TR302]]
|-
|-
|Yellow
|Yellow
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|-
|-
|Green
|Green
|
|[[media:GreenTR50.mas | TR50]]
|-
|-
|Blue
|Blue
|
|[[media:TR-TeamBlue-alignment-FINALV2.mas|TR58‎‎]]
|-
|-
|Purple
|Purple
|
|[[media:TRPrp_M1D8_062.mas | 6TR2]]
|-
|-
|}
|}
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|-
|-
|Red
|Red
|
|[[m‎edia:RedWF040revised.mas|040 revised 3.8.15 at 2:30pm]]
|-
|-
|Orange
|Orange
|
|[[Media:WF-Orange-alignment-FINAL.mas|040/274]]
|-
|-
|Yellow
|Yellow
|
|[[Media:274.C1.C6.C7.C10.C11.C12.C13.mas‎| 274]]
|-
|-
|Green
|Green
|
|[[Media:WFGrn_050_274.mas|050/274]]
|-
|-
|Blue
|Blue
|
|[[media:WF-Blue-Alignment-FINAL.mas‎‎‎|058/274 MEGA File]] <br> [[media:WF-Blue-Alignment-Tree.nwk‎‎|058/274 NWK File]] <br> [[media:WF-Blue-Alignment-Tree-Image.png‎|058/274 Tree Image]]<br>[[media:WF-Blue-Alignment-FINAL_274only_v2SKH.mas|Update:3/8 at 10:30am -- .mas bird 274 only]]<br>[[media:WF-Blue-Alignment-FINAL_58only_v2SKH.mas|Update: 3/8 at 10:30am -- .mas bird 58 only + updated names of bacteria strains]]
|-
|-
|Pink
|Pink
|
|[[media:WFPink290.mas|290]]
|-
|-
|Purple
|Purple
|
|[[Media:WFPrp040_274.mas]]
|-
|-
|Platinum
|Platinum
|
|[[media:Pt_WF_312_v2.mas]]
|-
|-
|}
|}
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|Orange
|Orange
|302
|302
| http://openwetware.org/images/c/ca/Pseudomonas.fluorescens.TROrg.302.1.txt
|[[media:Janthinobacterium.lividum.TROrg.302.16.txt|Bird302.C16]]
|
|[[media:Janthinobacterium.marseille.TROrg.Bird302.6.txt|Bird302.C6]]
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|[[media:Janthinobacterium.marseille.TROrg.Bird302.4.txt|Bird302.C4]]
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|[[media: Janthinobacterium.marseille.TROrg.Bird302.14.txt|Bird302.14]]
|
|[[media: Cupriavidus.basilensis.TROrg.302.13.txt| Bird302.C13]]
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|[[media: Janthinobacterium.lividum.TROrg.302.15.txt|Bird302.C15]]
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|[[media:Janthinobacterium.lividum.TROrg.302.11.txt|Bird302.C11]]
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|[[media:Janthinobacterium.lividum.TROrg.302.7.txt|Bird302.C7]]
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|[[media: Pseudomonas.fluorescens.TROrg.Bird302.8.txt|Bird302.C8]]
|
|[[media: TROrange302.xlsx|TROrange302.xlsx]]
|-
|-
|Yellow
|Yellow
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|Green
|Green
|50
|50
|[[media:Janthinbacterium.lividum.TRGrn.bird50.1.txt |50.C1]]
|[[media:Janthinobacterium.lividum.TRGrn.Bird50.2.txt |50.C2]]; [[media:Version2.txt |v2 - fixed sequence]]
|[[media: Janthinobacterium.lividum.TRGrn.bird50.3.txt |50.C3]]
|[[media: Shewanella.haliotis.TRGrn.bird50.4.txt |50.C4]]
|[[media:Pseudomonas.extremaustralis.TRGrn.bird50.5.txt|Bird50.C5]]
|[[media:Janthinobacterium.lividum.TRGrn.bird50.8.txt|Bird50.C8]]
|[[media:Janthinobacterium.lividum.TRBlu.Bird--58.9.txt|Bird50.C9]]
|[[media:Pseudomonas.flourescens.TRGren.Bird50.10.txt|Bird50.C10]]
|
|
|
|[[media:TRGreen050.xlsx |Greenbird50]]
|
|
|http://openwetware.org/images/e/e1/Pseudomonas.extremaustralis.TRGrn.bird50.5.txt
|http://openwetware.org/images/1/11/Janthinobacterium.lividum.TRGrn.bird50.8.txt
|http://openwetware.org/images/4/4b/Janthinobacterium.lividum.TRGrn.Bird50.9.txt
|http://openwetware.org/images/c/ce/Pseudomonas.flourescens.TRGren.Bird50.10.txt
|
|
|-
|-
|Blue
|Blue
|
|58
|
|[[media:Janthinobacterium.lividum.TRBlu.58.1V2.txt‎‎|Bird58.C1‎]]
|
|[[media:Janthinobacterium.lividum.TRBlu.58.2V2.txt‎‎|Bird58.C‎2]]
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|[[media:Janthinobacterium.lividum.TRBlu.58.4V2.txt‎‎‎|Bird58.C4]]
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|[[media:Janthinobacterium.lividum.TRBlu.58.5V2.txt‎‎|Bird58.C5‎]]
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|[[media:Janthinobacterium.lividum.TRBlu.Bird--58.9.txt|Bird58.C9]]
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|[[media:Janthinobacterium.lividum.TRBlu58.11.txt‎|Bird58.C11]]
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|[[media:Janthinobacterium.lividum.TRBlu.Bird-.58.13.txt‎|Bird58.C13]]
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|[[media:Janthinobacterium.lividum.TRBlu58.--15.txt|Bird58.C15‎]]
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|[[media:Janthinobacterium.lividum.TRBlu58.16.txt‎|Bird58.C16]]
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|[[media:TRBlu58-SHEET.ex.xlsx]]
|-
|-
|Purple
|Purple
|
|62
|http://openwetware.org/images/1/1e/Cupriavidus.basilensis.TRPrp.062.12.txt
|[[media:Cupriavidus.basilensis.TRPrp.062.12.txt |62.C12]]
|http://openwetware.org/images/e/ec/Janthinobacterium.lividum.TRPrp.062.1.txt
|[[media:Janthinobacterium.lividum.TRPrp.062.1.txt |62.C1]]
|http://openwetware.org/images/4/45/Janthinobacterium.lividum.TRPrp.062.9.txt
|[[media: Janthinobacterium.lividum.TRPrp.062.9.txt |62.C9]]
|http://openwetware.org/images/2/21/Janthinobacterium.lividum.TRPrp.062.15.txt
|[[media: Janthinobacterium.lividum.TRPrp.062.15.txt |62.C15]]
|http://openwetware.org/images/5/5e/Janthinobacterium.lividum.TRPrp.062.18.txt
|[[media: Janthinobacterium.lividum.TRPrp.062.18.txt | 62.C18]]
|http://openwetware.org/images/1/15/Janthinobacterium.lividum.TRPrp.062.14.txt
|[[media:Janthinobacterium.lividum.TRPrp.062.14.txt|62.C14]]
|
|[[media:Janthinobacterium.lividum.TRPrp.Bird-62.11.txt|Bird62.C11]]
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|[[media:Janthinobacterium.lividum.TRPrp.Bird-62.13.txt|Bird62.C13]]
|
|[[media:Pseudomonas.panacis.TRPrp.Bird-62.8.txt|Bird62.C8]]
|http://openwetware.org/images/d/d0/20.109%28s15%29_062.xlsx
|[[media:20.109(s15)_062.xlsx|TRPrp62]]
|-
|-
|}
|}
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! Sequence 9 (txt)
! Sequence 9 (txt)
! Species overview (xlsx)
! Species overview (xlsx)
! Sequence 10 (txt)
! Sequence 11 (txt)
! Sequence 12 (txt)
|-
|-
|Red
|Red
|040
|bad sequence
|[[Media:Janthinobacterium.lividium.WFRed.040.2-fixed.txt|040_C2]]
|[[Media:Janthinobacterium.lividium.WFRed.040.3-fixed.txt|040_C3]]
|[[Media:Shewanella.haliotis.WFRed.040.4-fixed.txt|040_C4]]
|[[Media:Janthinobacterium.lividium.WFRed.040.5.txt|040_C5]]
|[[Media:Raoultella.ornithinolytica.WFRed.040.11-fixed.txt|040_C11]]
|[[Media:Pseudomonas_extremaustralis.WFRed.040.12-fixed.txt|040_C12]]
|bad sequence
|
|
|
|[[Media:WFRed040.xlsx|040_species sheet]]
|
|
|
|
|
|
|
|
|
|-
|-
|Orange
|Orange
|040/274
|[[Media:Janthinobacterium.lividum.WFOrg.040.18.txt|040_C18]]
|[[Media:Shewanella.halitosis.WFRed.Bird040.15.txt|040_C15]]
|[[Media:Janthinobacterium.lividum.WFRed.Bird040.17.txt|040_C17]]
|[[Media:Pseudomonas.migulae.WFRed.Bird040.19.txt|040_C19]]
|[[Media:Janthinobacterium.lividum.WFOrg.274.16.txt|274_C16]]
|[[Media:Janthinobacterium.lividum.WFOrg.274.18.txt|274_C18]]
|[[Media:Janthinobacterium.lividum.WFYel.Bird274.20.txt|274_C20]]
|[[Media:Pseudomonas.fluorescens.WFYel.Bird274.19.txt|274_C19]]
|
|
|
|[[Media:WFOrangeSpeciesTemplate.xlsx|040/274 species sheet]]
|
|
|
|
|
|
|
|
|
|-
|-
|Yellow
|Yellow
|274
|[[Media:Janthinobacterium.lividum.WFYlw.274.C1.txt|274_C1]]
|[[Media:Janthinobacterium.lividum.WFYlw.274.6.txt‎|274_C6]]
|[[Media:Janthinobacterium.lividum.WFYlw.274.C7.txt‎|274_C7]]
|[[Media:Janthinobacterium.lividum.WFYlw.274.10.txt‎|274_C10]]
|[[Media:Klebsiella.oxytoca.WFYlw.274.C11.txt|274_C11]]
|[[Media:Glaciimonas.immobilis.WFYlw.274.C12.txt‎|274_C12]]
|[[Media:Janthinobacterium.lividum.WFYlw.274.C13.txt‎|274_C13]]
|[[Media:Janthinobacterium.lividum.WFYlw.274.15.txt‎|274_C15]]
|
|
|
|[[Media:274 species sheet.xlsx|274 species sheet]]
|
|
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|
|
|
|
|
|-
|-
|Green
|Green
|
|050/274
|
|[[media:Pseudomonas.fluorescens.WFGrn.050.6.txt|050_C6]]
|
|[[media:Janthinobacterium.lividum.WFGrn.050.7.txt|050_C7]]
|
|[[media:Pseudomonas.fluorescens.WFGrn.050.13.txt |050_C13]]
|
|[[media:Janthinobacterium.lividum.WFGrn.050.14.txt|050_C14]]
|
|[[media:Janthinobacterium.lividum.WFGrn.050.15.txt|050_C15]]
|
|[[media: Janthinobacterium.sp.Marseille.WFGrn.050.16.txt|050_C16]]
|
|[[media:Janthinobacterium.lividum.WFGrn.050.17.txt|050_17]]
|
|[[media:Janthinobacterium.lividum.WFGrn.050.20.txt|050_20]]
|
|[[media:Klebsiella.oxytoca.WFGrn.274.9.txt |274_FP_9]]
|
|[http://openwetware.org/images/6/6b/WFGreen050_274_%281%29.xlsx Species Overview]
|[[media:Klebsiella.oxytoca.WFGrn.274.10.txt |274_FP_10]]
|[[media:Klebsiella.oxytoca.WFGrn.274.11.txt| 274_FP_11]]
|[[media:Klebsiella.oxytoca.WFGrn.274.12.txt|274_FP_12]]
|-
|-
|Blue
|Blue
|058/274
|[[Media:WFBlue058C19.txt|058_C19]]
|[[Media:058_C17.txt|058_C17]]
|[[Media:058_C20.txt|058_C20]]
|[[Media:WFBlue274C1.txt|274_C1]]
|[[Media:274_C2.txt|274_C2]]
|[[Media:274_C4.txt|274_C4]]
|[[Media:WFBlue274C3S15.txt|274_C3]]
|[[Media:WFBlue274_C6.txt|274_C6]]
|
|
|
|[[Media:S15-M1D8-Species-Overview-WFBlue.xlsx|058/274]]
|
|
|
|
|
|
|
|
|
|-
|-
|Pink
|Pink
|290
|[[Media:Klebsiella.oxytoca.WFPnk.290F1.txt‎|290_F1]]
|[[Media:Pseudomonas.poae.WFPnk.290F2.txt|290_F2]]
|[[Media:Pseudomonas.graminis.WFPnk.290F3.txt‎|290_F3]]
|[[Media:Pseudomonas.libanensis.WFPnk.290F4.txt|290_F4]]
|[[Media:Klebsiella.oxytoca.WFPnk.290F5.txt‎|290_F5]]
|[[Media:Pseudomonas.fluorescens.WFPnk.290C6.txt‎|290_C6]]
|
|
|
|
|
|
|
|[[Media:WFPink290.xlsx‎|290]]
|
|
|
|
|
|
|
|-
|-
|Purple
|Purple
|040/274
|[[Media:WFPurple040C6.txt]]
|[[Media:WFPurple040C7.txt]]
|[[Media:WFPurple040C9.txt]]
|[[Media:WFPurple040C10.txt]]
|[[Media:WFPurple274FP7.txt]]
|[[Media:WFPurple274FP11.txt]]
|[[Media:WFPurple274FP12.txt]]
|
|
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|
|
|[[Media:WFPurple_BLAST.xlsx]]
|
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|
|
|
|-
|-
|Platinum
|Platinum
|312
|[[Media:Enterobacter.aerogenes.WFPt.312.1.txt|312_C1]]
|[[Media:Pseudomonas.azotoformans.WFPt.312.5.txt|312_C5]]
|[[Media:Klebsiella.oxytoca.WFPt.312.7.txt|312_C7]]
|[[Media:Pseudomonas.extremaustralis.WFPt.312.2.txt|312_C2]]
|[[Media:Pseudomonas.extremaustralis.WFPt.312.10.txt|312_C10]]
|[[Media:Pseudomonas.libanensis.WFPt.312.9.txt|312_C9]]
|[[Media:Klebsiella.oxytoca.WFPt.312.11.txt|312_C11]]
|[[Media:Pseudomonas.libanensis.WFPt.312.12.txt|312_C12]]
|[[Media:Pseudomonas.azotoformans.WFPt.312.6.txt|312_C6]]
|[[Media:Pseudomonas.azotoformans.WFPt.312.14.txt‎|312_C14]]
|
|
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|[[Media:WFPt312_v2.xlsx|312_All]]
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|-
|-
|}
|}
</center>
</center>

Latest revision as of 19:20, 10 March 2015

Upload alignment files here

All birds MEGA file + extra data from S14 (birds 312, 290, 274): MEGA file
ID Files that correspond to MEGA file above: ID file with spaces
ID file without spaces

Name your alignment file according to this example: WF-TeamColor-alignment-FINAL

T/R Groups Final MEGA File (upload .mas file)
Orange TR302
Yellow
Green TR50
Blue TR58‎‎
Purple 6TR2


W/F Groups Final MEGA File (upload .mas file)
Red 040 revised 3.8.15 at 2:30pm
Orange 040/274
Yellow 274
Green 050/274
Blue 058/274 MEGA File
058/274 NWK File
058/274 Tree Image
Update:3/8 at 10:30am -- .mas bird 274 only
Update: 3/8 at 10:30am -- .mas bird 58 only + updated names of bacteria strains
Pink 290
Purple Media:WFPrp040_274.mas
Platinum media:Pt_WF_312_v2.mas

Upload sequence files here

T/R Team Color 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) Sequence 9 (txt) Species overview (xlsx)
Orange 302 Bird302.C16 Bird302.C6 Bird302.C4 Bird302.14 Bird302.C13 Bird302.C15 Bird302.C11 Bird302.C7 Bird302.C8 TROrange302.xlsx
Yellow
Green 50 50.C1 50.C2; v2 - fixed sequence 50.C3 50.C4 Bird50.C5 Bird50.C8 Bird50.C9 Bird50.C10 Greenbird50
Blue 58 Bird58.C1‎ Bird58.C‎2 Bird58.C4 Bird58.C5‎ Bird58.C9 Bird58.C11 Bird58.C13 Bird58.C15‎ Bird58.C16 media:TRBlu58-SHEET.ex.xlsx
Purple 62 62.C12 62.C1 62.C9 62.C15 62.C18 62.C14 Bird62.C11 Bird62.C13 Bird62.C8 TRPrp62


W/F Team Color 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) Sequence 9 (txt) Species overview (xlsx) Sequence 10 (txt) Sequence 11 (txt) Sequence 12 (txt)
Red 040 bad sequence 040_C2 040_C3 040_C4 040_C5 040_C11 040_C12 bad sequence 040_species sheet
Orange 040/274 040_C18 040_C15 040_C17 040_C19 274_C16 274_C18 274_C20 274_C19 040/274 species sheet
Yellow 274 274_C1 274_C6 274_C7 274_C10 274_C11 274_C12 274_C13 274_C15 274 species sheet
Green 050/274 050_C6 050_C7 050_C13 050_C14 050_C15 050_C16 050_17 050_20 274_FP_9 Species Overview 274_FP_10 274_FP_11 274_FP_12
Blue 058/274 058_C19 058_C17 058_C20 274_C1 274_C2 274_C4 274_C3 274_C6 058/274
Pink 290 290_F1 290_F2 290_F3 290_F4 290_F5 290_C6 290
Purple 040/274 Media:WFPurple040C6.txt Media:WFPurple040C7.txt Media:WFPurple040C9.txt Media:WFPurple040C10.txt Media:WFPurple274FP7.txt Media:WFPurple274FP11.txt Media:WFPurple274FP12.txt Media:WFPurple_BLAST.xlsx
Platinum 312 312_C1 312_C5 312_C7 312_C2 312_C10 312_C9 312_C11 312_C12 312_C6 312_C14 312_All
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