Tom Jonesman

8 Questions 12 Answers 0 Followers

Questions related from Tom Jonesman

Free T-RFLP analysis software?

I am looking for a free, online software that can be used for the analysis of T-RFLP data. I have come across T-REX, but this requires the upload of files exported from software that is not free....

12 December 2013 5,607 3 View

Is there a way to return upper and lower values of a simulated envelope?

The attached figure is a mark correlation function produced by the spatstat package in R. The summary returned from the object used to produce this figure is as follows: r theo...

11 November 2013 5,167 3 View

Which outgroup and which genes are used for angiosperm phylogeny?

I need to construct a phylogenetic tree for 4 grasses (Festuca, Holcus, Anthoxanthum and Agrostis) and 4 forbs (Leucanthemum, Centaurea, Rumex and Plantago), but have little experience in plant...

11 November 2013 4,907 3 View

Advice on measuring soil environmental parameters?

I have collected soil samples of roughly 56 cubic centimetres each. I have dried them and now need to determine the following parameters: 1. pH 2. Total Organic Carbon 3. Inorganic carbon 4....

09 September 2013 8,745 4 View

Does anybody use the primers AML1 and AML2 instead of AM1 and NS31 in arbuscular mycorrhizal fungal research?

Instead of the universal eukaryotic primer NS31 and the AM-specific primer AM1, I am wondering if anyone has used the primers developed by Lee et al (2008) that amplify a much higher proportion of...

06 June 2013 9,241 6 View

Generating Rank abundance curves in R?

I'm using the BiodiversityR package to generate rank abundance curves. The following code scales the y axis as proportional abundance (species abundance/total abundance). The y axis then...

06 June 2013 5,813 5 View

What do you use to incubate restriction digestion reactions?

I have been using a Hybaid Shake n' stack style incubator (http://www.fishersci.com.sg/product_details.asp?nid=761), but was wondering if anybody uses a water bath instead, perhaps for improved...

06 June 2013 3,866 44 View

Optimising PCR with fluorescently labelled primers.

For downstream fragment analysis (T-RFLP), I am running PCRs with primers labelled with the fluorescent tags HEX and 6-FAM. After having some trouble gaining enough product, I now do a primary PCR...

04 April 2013 6,752 5 View