Talk:20.109(S13):Phylogenetic analysis (Day7): Difference between revisions
Sarah N. Yu (talk | contribs) |
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 21: | Line 80: | ||
|- | |- | ||
|Red | |Red | ||
|Nick | |||
|702 | |||
|[[Media:TR-Red_702-C1.txt]] | |||
|[[Media:TR-Red_702-C2.txt]] | |||
|[[Media:TR-Red_702-C3.txt]] | |||
| | | | ||
| | | | ||
| | | | ||
| | |[[Media:TR-Red_702-C7.txt]] | ||
| | |[[Media:TR-Red_702-C8.txt]] | ||
| | |[[Media:TR-Red-Species.xlsx]] | ||
| | |[[Media:TR-Red-Blue-702.mas]] | ||
| | |[[Media:TR-Blue-Red-tree.pdf]] | ||
|- | |- | ||
|Red | |Red | ||
Line 51: | Line 110: | ||
|- | |- | ||
|Orange | |Orange | ||
|Daphne, Stas | |||
|712 | |||
| | | | ||
|[[Media:TR-Orange_712-C2.txt]] | |||
| | | | ||
| | | | ||
|[[Media:TR-Org_712-C5.txt]] | |||
| | | | ||
| | |[[Media:TR-Org_712-C7.txt]] | ||
| | |[[Media:TR-Org_712-C8.txt]] | ||
| | |[[Media:TR-Orange_712.xlsx]] | ||
| | |[[Media:TR-712-Alignment.mas]] | ||
| | |[[Media:TR-712-Alignment.pdf]] | ||
|- | |- | ||
|Orange | |Orange | ||
Line 81: | Line 140: | ||
|- | |- | ||
|Yellow | |Yellow | ||
|Ebaa | |||
|664 (seq order corrected) | |||
|[[Media: Updated TR-Yellow_664-C1.txt]] | |||
| | | | ||
| | | | ||
|[[Media: Updated TR-Yellow_664-C4.txt]] | |||
| | | | ||
| | | | ||
| | | | ||
| | |[[Media: Updated TR-Yellow_664-C8.txt]] | ||
| | |[[Media: 664_S13-M1D7-template.xlsx]] | ||
| | |[[Media: Updated WFTR-664-alignment.mas]] | ||
| | |[[Media: New Updated WFTR-664-tree.pdf]] | ||
|- | |- | ||
|Yellow | |Yellow | ||
|Dominique | |||
|739 (everything should be in correct seq order) | |||
| | | | ||
| | |[[Media: TR-Yellow_739-C2f.txt]] | ||
| | |[[Media: TR-Yellow_739-C3.txt]] | ||
| | |[[Media: TR-Yellow_739-C4f.txt]] | ||
| | |[[Media: TR-Yellow_739-C5f.txt]] | ||
| | |[[Media: TR-Yellow_739-C6f.txt]] | ||
| | |[[Media: TR-Yellow_739-C7.txt]] | ||
| | |[[Media: TR-Yellow_739-C8f.txt]] | ||
| | |[[Media: 739_S13-M1D7-template.xlsx]] | ||
| | |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]] | ||
| | |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 | ||
|Jesse | |||
|405 | |||
|[[Media: TR-Green_405-C1.txt]] | |||
|[[Media: TR-Green_405-C2.txt]] | |||
|[[Media: TR-Green_405-C3-edit.txt]] | |||
|[[Media: TR-Green_405-C4-edit.txt]] | |||
| | | | ||
|[[Media: TR-Green_405-C6-edit.txt]] | |||
|[[Media: TR-Green_405-C7-edit.txt]] | |||
| | | | ||
| | |[[Media: TR-Green-405-Sepecies Overview.xlsx]] | ||
| | |[[Media: WF-405_Alignment_with_TR_edited.mas]] | ||
| | |[[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 156: | Line 215: | ||
|- | |- | ||
|Blue | |Blue | ||
|Noa | |||
|702 | |||
| | | | ||
| | | | ||
| | | | ||
|[[Media:TR-Blue-702-C4.txt]] | |||
|[[Media:TR-Blue-702-C5.txt]] | |||
|[[Media:TR-Blue-702-C6.txt]] | |||
| | | | ||
| | |[[Media:TR-Blue-702-C8.txt]] | ||
| | |[[Media:TR-Blue-702.xlsx]] | ||
| | |[[Media:TR-Red-Blue-702.mas]] | ||
| | |[[Media:TR-Blue-Red-tree.pdf]] | ||
|- | |- | ||
|Pink | |Pink | ||
|Justin & Arturo | |||
|709 | |||
| | | | ||
| | | | ||
| | | | ||
| | | | ||
|[[Media:TR-Pink_709-C5B.txt]] | |||
|[[Media:TR-Pink_709-C6B.docx]] | |||
| | | | ||
| | | | ||
| | | | ||
| | |[[Media:TR-Pink_709B.xlsx]] | ||
| | | | ||
|- | |- | ||
|Pink | |Pink | ||
| | | | ||
| | |709 | ||
| | |[[Media: B1.txt]] | ||
| | | | ||
| | | | ||
Line 211: | Line 270: | ||
|[[Media:TR-Purple_739-C7.txt]] | |[[Media:TR-Purple_739-C7.txt]] | ||
|[[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]] more complete file in Dominique's box | ||
| | | | ||
|- | |- | ||
|Purple | |Purple | ||
|Mitali | |||
|664 | |||
| | | | ||
|[[Media:TR-Purple_664-C2.txt]] | |||
| | | | ||
| | | | ||
|[[Media:TR-Purple_664-C5.txt]] | |||
| | | | ||
| | |[[Media:TR-Purple_664-C7.txt]] | ||
| | |[[Media:TR-Purple_664-C8.txt]] | ||
| | |[[Media:TR-Purple_664-MK.xlsx]] | ||
| | |[[Media: WFTR-664-alignment.mas]] | ||
| | |[[Media: WFTR-664-tree.pdf]] | ||
|- | |- | ||
|Platinum | |Platinum | ||
Line 241: | Line 300: | ||
| | | | ||
| | | | ||
| | |[[Media:TR_platinum_732.xlsx]] | ||
| | |[[Media:emily and nikki m5 data.mas]] | ||
| | | | ||
|- | |- | ||
|Platinum | |Platinum | ||
| [[Media: | |Katie | ||
| | |405 | ||
| | |<font color=red> Updated AGA start: </font> [[Media:TR_Platinum_405_c1_edited.txt]] | ||
| | | - | ||
| | |[[Media:TR_Platinum_405_c3.txt]] | ||
| | | - | ||
| | |[[Media:TR_Platinum_405_c5.txt]] | ||
| | |[[Media:TR_Platinum_405_c6.txt]] | ||
| | | - | ||
| | |<font color = red> Updated AGA start: </font> [[Media:TR_Platinum_405_c8_edited.txt]] | ||
| | |[[Media:KB_TR_Platinum.xlsx]] | ||
| | ||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]], <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 288: | 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 | ||
|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 | |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 | |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 | |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 | |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 | |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 | |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 | |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 | |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 | |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 | |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 | ||
| | |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 | |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]] | ||
| | | | ||
| | | | ||
Line 531: | Line 591: | ||
==T/R microsporidia gels== | ==T/R microsporidia gels== | ||
[[Image:S13-M1D7-TR-Gel1.jpg|thumb|left|300px|Gel 1]] | [[Image:S13-M1D7-TR-Gel1.jpg|thumb|left|300px|Gel 1]] | ||
Line 542: | Line 601: | ||
==W/F microsporidia gels== | ==W/F microsporidia gels== | ||
[[Image:S13-M1D7-WF-Gel2.jpg|thumb|left|300px|Gel 2]] | |||
[[Image:S13-M1D7-WF-Gel3.jpg|thumb|center|300px|Gel 3]] | |||
[[Image:S13-M1D7-WF-Gel4.jpg|thumb|left|300px|Gel 4]] | |||
[[Image:S13-M1D7-WF-Gel1-bright.jpg|thumb|center|300px|Gel 1, bright]] | |||
[[Image:S13-M1D7-WF-Gel1-dim.jpg|thumb|left|300px|Gel 1, dim]] | |||
<br style="clear:both;"/> |
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