Talk:20.109(S13):Phylogenetic analysis (Day7)

From OpenWetWare

Revision as of 17:19, 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)

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.

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

Gel 1

Gel 2, bright

Gel 3

Gel 4

Image:S13-M1D7-TR-Gel2-dim.jpg

W/F microsporidia gels

Gel 2

Gel 3

Gel 4

Gel 1, bright

Gel 1, dim