Talk:20.109(S13):Phylogenetic analysis (Day7): Difference between revisions
Sarah N. Yu (talk | contribs) |
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==General notes and updates== | |||
I've added five additional #709 sequences to the existing alignment file, and posted the final alignment file and tree. | |||
A student who is recovering from illness may also post a few additional #712 sequences and an updated alignment and tree file this weekend. She will not delete the old file, since many of you are already using it, but will simply add hers as another option to use in your reports. | |||
Consider doing a "watch" on this page so you know when it changes. | |||
I'd also like to link my Excel species worksheet [[Media: S13-M1D7-709-extra-clones.xlsx | right here]]. You can see that I had a few interesting decisions to make, which perhaps could apply to some of you as well. I don't expect any more changes to the trees at this point, but perhaps for the revision you can revisit your choices. More specifically: (1) in some cases I had only partial sequence, so I made naming decisions at a higher taxonomic level; (2) in one case the top choice was misleading because it was a partial sequence; (3) One sequence was longer than usual, which took a bit of extra searching to process during the trimming stage, because there was so little sequence overlap. | |||
[[User:AgiStachowiak|AgiStachowiak]] 16:19, 8 March 2013 (EST) | |||
An updated version of the #739 alignment file & tree was posted to get rid of duplicates of some insert sequences. | |||
[[User:Sarah N. Yu|Sarah N. Yu]] 21:13, 8 March 2013 (EST) | |||
==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. | |||
{| border="1" | |||
|Sample # | |||
|Alignment file (.mas) | |||
|Tree file (.pdf) | |||
|- | |||
|702 | |||
|[[Media: Final_702_Alignment.mas]] | |||
|[[Media: Final_702_PhyloTree.pdf]] | |||
|- | |||
|709 | |||
|[[Media: 709-final-alignment.mas]] | |||
|[[Media: S13_709-final-tree.pdf]] | |||
|- | |||
|712 | |||
|[[Media: Final_712_Alignment.mas]] | |||
|[[Media: Final_712_PhyloTree.pdf]] | |||
|- | |||
|716 | |||
|No clones worked | |||
|No clones worked | |||
|- | |||
|405 | |||
|[[Media: Final_405_Alignment.mas]] | |||
|[[Media: Final_405_PhyloTree.pdf]] | |||
|- | |||
|664 | |||
|[[Media: Updated WFTR-664-alignment.mas]] | |||
|[[Media: New Updated WFTR-664-tree.pdf]] | |||
|- | |||
|732 | |||
|[[Media: 732-FinalAlignment.mas]] | |||
|[[Media: 732-FinalTree.pdf]] | |||
|- | |||
|739 | |||
|[[Media: FINAL-739-MA-alignment.mas]] | |||
|[[Media: FINAL-739-Phylogenetic-Tree.pdf]] | |||
|- | |||
|} | |||
==T/R microbiome== | ==T/R microbiome== | ||
Line 23: | Line 82: | ||
|Nick | |Nick | ||
|702 | |702 | ||
|[[Media:TR- | |[[Media:TR-Red_702-C1.txt]] | ||
|[[Media:TR- | |[[Media:TR-Red_702-C2.txt]] | ||
|[[Media:TR- | |[[Media:TR-Red_702-C3.txt]] | ||
| | | | ||
| | | | ||
| | | | ||
|[[Media:TR- | |[[Media:TR-Red_702-C7.txt]] | ||
|[[Media:TR- | |[[Media:TR-Red_702-C8.txt]] | ||
|[[Media:TR-Red-Species.xlsx]] | |[[Media:TR-Red-Species.xlsx]] | ||
|[[Media:TR-Red-Blue-702.mas]] | |[[Media:TR-Red-Blue-702.mas]] | ||
Line 57: | Line 116: | ||
| | | | ||
| | | | ||
|[[Media:TR- | |[[Media:TR-Org_712-C5.txt]] | ||
| | | | ||
|[[Media:TR- | |[[Media:TR-Org_712-C7.txt]] | ||
|[[Media:TR- | |[[Media:TR-Org_712-C8.txt]] | ||
|[[Media:TR-Orange_712.xlsx]] | |[[Media:TR-Orange_712.xlsx]] | ||
|[[Media:TR-712- | |[[Media:TR-712-Alignment.mas]] | ||
|[[Media:TR-712-Alignment.pdf]] | |[[Media:TR-712-Alignment.pdf]] | ||
|- | |- | ||
Line 82: | Line 141: | ||
|Yellow | |Yellow | ||
|Ebaa | |Ebaa | ||
|664 | |664 (seq order corrected) | ||
|[[Media: TR-Yellow_664-C1.txt]] | |[[Media: Updated TR-Yellow_664-C1.txt]] | ||
| | | | ||
| | | | ||
|[[Media: TR-Yellow_664-C4.txt]] | |[[Media: Updated TR-Yellow_664-C4.txt]] | ||
| | | | ||
| | | | ||
| | | | ||
|[[Media: TR-Yellow_664-C8.txt]] | |[[Media: Updated TR-Yellow_664-C8.txt]] | ||
|[[Media: 664_S13-M1D7-template.xlsx]] | |[[Media: 664_S13-M1D7-template.xlsx]] | ||
| | |[[Media: Updated WFTR-664-alignment.mas]] | ||
| | |[[Media: New Updated WFTR-664-tree.pdf]] | ||
|- | |- | ||
|Yellow | |Yellow | ||
|Dominique | |Dominique | ||
|739 | |739 (everything should be in correct seq order) | ||
| | | | ||
|[[Media: TR-Yellow_739- | |[[Media: TR-Yellow_739-C2f.txt]] | ||
|[[Media: TR-Yellow_739- | |[[Media: TR-Yellow_739-C3.txt]] | ||
|[[Media: TR-Yellow_739- | |[[Media: TR-Yellow_739-C4f.txt]] | ||
|[[Media: TR-Yellow_739- | |[[Media: TR-Yellow_739-C5f.txt]] | ||
|[[Media: TR-Yellow_739- | |[[Media: TR-Yellow_739-C6f.txt]] | ||
|[[Media: TR-Yellow_739-C7.txt]] | |[[Media: TR-Yellow_739-C7.txt]] | ||
|[[Media: TR-Yellow_739- | |[[Media: TR-Yellow_739-C8f.txt]] | ||
|[[Media: 739_S13-M1D7-template.xlsx]] | |[[Media: 739_S13-M1D7-template.xlsx]] | ||
|[[Media: TR-739-alignment.mas]] | |Alignment of all 739 from TR [[Media: TR-739-alignment.mas]] Alignment of TR+ (Jenny's-WF) 739 [[Media:TR-(JW-WF)-739-alignment.mas]] new version still w/ TR + Jenny's-WF [[Media:TR-(JW-WF)-739-alignmentedit.mas]] | ||
|[[Media:TR-739-tree.pdf]] | |Tree of all 739 clones from TR [[Media:TR-739-tree.pdf]] Tree of TR + (Jenny's-WF) 739 [[Media: TR+(JW-WF)-739-tree.pdf]] new version still w/ TR + Jenny's-WF [[Media:TR + (JW-WF)-739-treeedit.pdf]] | ||
|- | |- | ||
|Green | |Green | ||
Line 115: | Line 174: | ||
|[[Media: TR-Green_405-C1.txt]] | |[[Media: TR-Green_405-C1.txt]] | ||
|[[Media: TR-Green_405-C2.txt]] | |[[Media: TR-Green_405-C2.txt]] | ||
|[[Media: TR-Green_405-C3.txt]] | |[[Media: TR-Green_405-C3-edit.txt]] | ||
|[[Media: TR-Green_405-C4.txt]] | |[[Media: TR-Green_405-C4-edit.txt]] | ||
| | | | ||
|[[Media: TR-Green_405-C6.txt]] | |[[Media: TR-Green_405-C6-edit.txt]] | ||
|[[Media: TR-Green_405-C7.txt]] | |[[Media: TR-Green_405-C7-edit.txt]] | ||
| | | | ||
|[[Media: TR-Green-405-Sepecies Overview.xlsx]] | |[[Media: TR-Green-405-Sepecies Overview.xlsx]] | ||
|[[Media: | |[[Media: WF-405_Alignment_with_TR_edited.mas]] | ||
|[[Media: TR | |[[Media: Phylogeny Tree TF and Steve only with edits to TR.pdf]] | ||
|- | |- | ||
|Green | |Green | ||
|Nikki | |||
|732 | |||
|[[Media: TR-Grn_732-C1.txt]] | |||
|[[Media: TR-Grn_732-C2.txt]] | |||
|[[Media: TR-Grn_732-C3.txt]] | |||
|[[Media: TR-Grn_732-C4.txt]] | |||
| | | | ||
|[[Media: TR-Grn_732-C6.txt]] | |||
|[[Media: TR-Grn_732-C7.txt]] | |||
| | | | ||
| | |[[Media: TR-Grn_732.xlsx]] | ||
| | |<font color = red> Confirmed AGA start</font> [[Media: TR-732-Alignment.mas]] | ||
| | |[[Media: TR-732-Tree.pdf]] | ||
|- | |- | ||
|Blue | |Blue | ||
Line 212: | Line 271: | ||
|[[Media:TR-Purple_739-C8.txt]] | |[[Media:TR-Purple_739-C8.txt]] | ||
|[[Media:S13-M1D7-template-Sarah Yu.xlsx]] | |[[Media:S13-M1D7-template-Sarah Yu.xlsx]] | ||
|[[Media:module1.mas]] | |[[Media:module1.mas]] more complete file in Dominique's box | ||
| | | | ||
|- | |- | ||
Line 227: | Line 286: | ||
|[[Media:TR-Purple_664-C8.txt]] | |[[Media:TR-Purple_664-C8.txt]] | ||
|[[Media:TR-Purple_664-MK.xlsx]] | |[[Media:TR-Purple_664-MK.xlsx]] | ||
| | |[[Media: WFTR-664-alignment.mas]] | ||
| | |[[Media: WFTR-664-tree.pdf]] | ||
|- | |- | ||
|Platinum | |Platinum | ||
Line 248: | Line 307: | ||
|Katie | |Katie | ||
|405 | |405 | ||
|[[Media: | |<font color=red> Updated AGA start: </font> [[Media:TR_Platinum_405_c1_edited.txt]] | ||
| - | | - | ||
|[[Media:TR_Platinum_405_c3.txt]] | |[[Media:TR_Platinum_405_c3.txt]] | ||
Line 255: | Line 314: | ||
|[[Media:TR_Platinum_405_c6.txt]] | |[[Media:TR_Platinum_405_c6.txt]] | ||
| - | | - | ||
|[[Media: | |<font color = red> Updated AGA start: </font> [[Media:TR_Platinum_405_c8_edited.txt]] | ||
|[[Media:KB_TR_Platinum.xlsx]] | |[[Media:KB_TR_Platinum.xlsx]] | ||
||Katie before combining with Jesse: [[Media:KatieJesseSession.mas]], Katie and Jesse (405) Aligned: [[Media: TR-405 alignment.mas]] | ||Katie before combining with Jesse: [[Media:KatieJesseSession.mas]], Katie and Jesse (405) Aligned: [[Media: TR-405 alignment.mas]],<font color = red> Katie, Jesse and Steve C. alignment:</font> [[Media: WF-405 Alignment with TR edited.mas]] | ||
|Katie and Jesse (405) finished tree - [[Media: TR-405-PhyloTree.pdf]] | |Katie and Jesse (405) finished tree - [[Media: TR-405-PhyloTree.pdf]], <font color = red> Katie,Jesse Steve corrected tree (waiting on 4th 405 sample)- </font> [[Media: 405 Phylogeny Tree TF and Steve only with edits to TR.pdf]] | ||
| | | | ||
|- | |- | ||
Line 289: | Line 348: | ||
|- | |- | ||
|Red | |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 | |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 | |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 | |Orange | ||
Line 345: | Line 404: | ||
|[[Media: WF-Orange_712-C8.txt]] | |[[Media: WF-Orange_712-C8.txt]] | ||
|[[Media: WF-Orange_712.xlsx]] | |[[Media: WF-Orange_712.xlsx]] | ||
|[[Media: | |[[Media: FULL 712 Alignment(TR_Orange + WF_Blue, Orange, Pink).mas]] | ||
|[[Media: | |[[Media: FULL 712 PhyloTree (TR_Orange + WF_Orange, Blue, Pink).pdf]] | ||
|- | |- | ||
|Yellow | |Yellow | ||
Line 375: | Line 434: | ||
| | | | ||
|[[Media: WF-Yellow_664.xlsx]] | |[[Media: WF-Yellow_664.xlsx]] | ||
|[[Media: | |[[Media: WFTR-664-Alignment.mas]] | ||
|[[Media: WRTF-664-tree.pdf]] | |||
|- | |- | ||
|Green | |Green | ||
Line 435: | Line 494: | ||
| [[Media: WF-Blue_702-C8.txt]] | | [[Media: WF-Blue_702-C8.txt]] | ||
| [[Media: WF-Blue_702.xlsx]] | | [[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 | |Pink | ||
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| | | | ||
| | | | ||
|[[Media: WF- | |[[Media: WF-Pink_712C4.txt]] | ||
|[[Media: WF- | |[[Media: WF-Pink_712C5.txt]] | ||
|[[Media: WF- | |[[Media: WF-Pink_712C6.txt]] | ||
|[[Media: WF- | |[[Media: WF-Pink_712C7.txt]] | ||
|[[Media: WF- | |[[Media: WF-Pink_712C8.txt]] | ||
|[[Media: WF-Pink_712.xlsx]] | |[[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 | |Pink | ||
Line 480: | Line 539: | ||
|[[Media: WF-Purple_664-C8.txt]] | |[[Media: WF-Purple_664-C8.txt]] | ||
|[[Media: WF-Purple_664.xlsx]] | |[[Media: WF-Purple_664.xlsx]] | ||
|[[Media: | |[[Media: WFTR-664-Alignment.mas]] | ||
| | |[[Media: WRTF-664-tree.pdf]] | ||
|- | |- | ||
|Purple | |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 | |Platinum | ||
Line 509: | Line 568: | ||
|[[Media: plt-7.txt]] | |[[Media: plt-7.txt]] | ||
|[[Media: 8.txt]] | |[[Media: 8.txt]] | ||
| | |[[Media: WF_732_sequence_data.xlsx]] | ||
|[[Media: WF-732 Alignment (TR-Platinum, WF-Green, Platinum).mas]] | |[[Media: WF-732 Alignment (TR-Platinum, WF-Green, Platinum).mas]] | ||
|[[Media: WF-732-PhyloTree (TR-Platinum + WF-Green, Platinum).pdf]] | |[[Media: WF-732-PhyloTree (TR-Platinum + WF-Green, Platinum).pdf]] | ||
|- | |- | ||
|Platinum | |Platinum | ||
|Shanthi Ravi | |||
|405 | |||
| | | | ||
|[[Media: WF-PLT_405-C2.txt]] | |||
|[[Media: WF-PLT_405-C3.txt]] | |||
|[[Media: WF-PLT_405-C4.txt]] | |||
|[[Media: WF-PLT_405-C5.txt]] | |||
| | | | ||
| | |[[Media: WF-PLT_405-C7.txt]] | ||
| | |[[Media: WF-PLT_405-C8.txt]] | ||
| | |[[Media: WF-PLT_405.xlxs]] | ||
| | | | ||
| | | |
Latest revision as of 19:13, 8 March 2013
General notes and updates
I've added five additional #709 sequences to the existing alignment file, and posted the final alignment file and tree.
A student who is recovering from illness may also post a few additional #712 sequences and an updated alignment and tree file this weekend. She will not delete the old file, since many of you are already using it, but will simply add hers as another option to use in your reports.
Consider doing a "watch" on this page so you know when it changes.
I'd also like to link my Excel species worksheet right here. You can see that I had a few interesting decisions to make, which perhaps could apply to some of you as well. I don't expect any more changes to the trees at this point, but perhaps for the revision you can revisit your choices. More specifically: (1) in some cases I had only partial sequence, so I made naming decisions at a higher taxonomic level; (2) in one case the top choice was misleading because it was a partial sequence; (3) One sequence was longer than usual, which took a bit of extra searching to process during the trimming stage, because there was so little sequence overlap.
AgiStachowiak 16:19, 8 March 2013 (EST)
An updated version of the #739 alignment file & tree was posted to get rid of duplicates of some insert sequences.
Sarah N. Yu 21:13, 8 March 2013 (EST)
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) |
702 | Media: Final_702_Alignment.mas | Media: Final_702_PhyloTree.pdf |
709 | Media: 709-final-alignment.mas | Media: S13_709-final-tree.pdf |
712 | Media: Final_712_Alignment.mas | Media: Final_712_PhyloTree.pdf |
716 | No clones worked | No clones worked |
405 | Media: Final_405_Alignment.mas | Media: Final_405_PhyloTree.pdf |
664 | Media: Updated WFTR-664-alignment.mas | Media: New Updated WFTR-664-tree.pdf |
732 | Media: 732-FinalAlignment.mas | Media: 732-FinalTree.pdf |
739 | Media: FINAL-739-MA-alignment.mas | Media: FINAL-739-Phylogenetic-Tree.pdf |
T/R microbiome
Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].
W/F microbiome
Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].
T/R microsporidia gels
W/F microsporidia gels