Talk:20.109(S15):Phylogentic analysis (Day8): Difference between revisions
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==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 | ||
Line 14: | Line 17: | ||
|- | |- | ||
|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 | ||
| | |[[media:Janthinobacterium.lividum.TROrg.302.16.txt|Bird302.C16]] | ||
| | |[[media:Janthinobacterium.marseille.TROrg.Bird302.6.txt|Bird302.C6]] | ||
| | |[[media:Janthinobacterium.marseille.TROrg.Bird302.4.txt|Bird302.C4]] | ||
| | |[[media: Janthinobacterium.marseille.TROrg.Bird302.14.txt|Bird302.14]] | ||
| | |[[media: Cupriavidus.basilensis.TROrg.302.13.txt| Bird302.C13]] | ||
| | |[[media: Janthinobacterium.lividum.TROrg.302.15.txt|Bird302.C15]] | ||
| | |[[media:Janthinobacterium.lividum.TROrg.302.11.txt|Bird302.C11]] | ||
| | |[[media:Janthinobacterium.lividum.TROrg.302.7.txt|Bird302.C7]] | ||
| | |[[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]] | ||
| | |||
|- | |- | ||
|Blue | |Blue | ||
| | |58 | ||
| | |[[media:Janthinobacterium.lividum.TRBlu.58.1V2.txt|Bird58.C1]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu.58.2V2.txt|Bird58.C2]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu.58.4V2.txt|Bird58.C4]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu.58.5V2.txt|Bird58.C5]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu.Bird--58.9.txt|Bird58.C9]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu58.11.txt|Bird58.C11]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu.Bird-.58.13.txt|Bird58.C13]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu58.--15.txt|Bird58.C15]] | ||
| | |[[media:Janthinobacterium.lividum.TRBlu58.16.txt|Bird58.C16]] | ||
| | |[[media:TRBlu58-SHEET.ex.xlsx]] | ||
|- | |- | ||
|Purple | |Purple | ||
| | |62 | ||
| | |[[media:Cupriavidus.basilensis.TRPrp.062.12.txt |62.C12]] | ||
| | |[[media:Janthinobacterium.lividum.TRPrp.062.1.txt |62.C1]] | ||
| | |[[media: Janthinobacterium.lividum.TRPrp.062.9.txt |62.C9]] | ||
| | |[[media: Janthinobacterium.lividum.TRPrp.062.15.txt |62.C15]] | ||
| | |[[media: Janthinobacterium.lividum.TRPrp.062.18.txt | 62.C18]] | ||
| | |[[media:Janthinobacterium.lividum.TRPrp.062.14.txt|62.C14]] | ||
| | |[[media:Janthinobacterium.lividum.TRPrp.Bird-62.11.txt|Bird62.C11]] | ||
| | |[[media:Janthinobacterium.lividum.TRPrp.Bird-62.13.txt|Bird62.C13]] | ||
| | |[[media:Pseudomonas.panacis.TRPrp.Bird-62.8.txt|Bird62.C8]] | ||
| | |[[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]] | ||
| | |||
|- | |- | ||
|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]] | |||
| | | | ||
| | | | ||
| | |[[Media:WFPurple_BLAST.xlsx]] | ||
|- | |- | ||
|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]] | |||
| | | | ||
| | |[[Media:WFPt312_v2.xlsx|312_All]] | ||
| | |||
|- | |- | ||
|} | |} | ||
</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 |