Talk:20.109(S13):Phylogenetic analysis (Day7): Difference between revisions
Sarah N. Yu (talk | contribs) |
|||
| (28 intermediate revisions by 9 users not shown) | |||
| Line 1: | Line 1: | ||
==General notes== | ==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== | ==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. | 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" | {| border="1" | ||
| Line 25: | Line 29: | ||
|- | |- | ||
|709 | |709 | ||
| | |[[Media: 709-final-alignment.mas]] | ||
| | |[[Media: S13_709-final-tree.pdf]] | ||
|- | |- | ||
|712 | |712 | ||
| Line 37: | Line 41: | ||
|- | |- | ||
|405 | |405 | ||
| | |[[Media: Final_405_Alignment.mas]] | ||
| | |[[Media: Final_405_PhyloTree.pdf]] | ||
|- | |- | ||
|664 | |664 | ||
| | |[[Media: Updated WFTR-664-alignment.mas]] | ||
| | |[[Media: New Updated WFTR-664-tree.pdf]] | ||
|- | |- | ||
|732 | |732 | ||
| | |[[Media: 732-FinalAlignment.mas]] | ||
| | |[[Media: 732-FinalTree.pdf]] | ||
|- | |- | ||
| | |739 | ||
| | |[[Media: FINAL-739-MA-alignment.mas]] | ||
| | |[[Media: FINAL-739-Phylogenetic-Tree.pdf]] | ||
|- | |- | ||
|} | |} | ||
| Line 137: | 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: WFTR-664-alignment.mas]] | |[[Media: Updated WFTR-664-alignment.mas]] | ||
|[[Media: WFTR-664-tree.pdf]] | |[[Media: New Updated WFTR-664-tree.pdf]] | ||
|- | |- | ||
|Yellow | |Yellow | ||
| Line 181: | Line 185: | ||
|- | |- | ||
|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 370: | Line 374: | ||
|[[Media: WF_red_702_24.txt]] | |[[Media: WF_red_702_24.txt]] | ||
|[[Media: WF-Red-702.xlsx]] | |[[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 | ||
| Line 386: | Line 390: | ||
|[[Media: S13-M1D7-WF-Orange-Mockett.xlsx]] | |[[Media: S13-M1D7-WF-Orange-Mockett.xlsx]] | ||
|[[Media: WF-709-alignment-org.mas]] | |[[Media: WF-709-alignment-org.mas]] | ||
| | |[[Media: FULL 709 PhyloTree (TR Pink, WF Pink + Orange)]] | ||
|- | |- | ||
|Orange | |Orange | ||
| Line 430: | Line 434: | ||
| | | | ||
|[[Media: WF-Yellow_664.xlsx]] | |[[Media: WF-Yellow_664.xlsx]] | ||
|[[Media: | |[[Media: WFTR-664-Alignment.mas]] | ||
|[[Media: | |[[Media: WRTF-664-tree.pdf]] | ||
|- | |- | ||
|Green | |Green | ||
| Line 506: | Line 510: | ||
|[[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).mas]] | ||
| | |[[Media: WF-712-Alignment(WF_Blue+TR_Orange+WF_Pink).pdf]] | ||
|- | |- | ||
|Pink | |Pink | ||
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
