I am using R package, "SPIDER" (SPecies IDentity and Evolution), I got its tutorial, which describes analysis for: anoteropsis, dolomedes and sarkar files (input file .rda). The tutorial works fine, even my dataset (FASTA format) was loaded sucessfully.
Following same tutorial with my data, at the step of species vector, i got stuck.. (I am new to R package SPIDER, even new to commands). How to assign dimnames,
Command given in tutorial: (head(dimnames(anoteropsis)[[1]]))
I want to follow the tutorial with my data, can suggest to me how to assign dimnames to my FASTA file, how should i proceed further?
Need help through the process,
(Attachment: Tutorial.Zip
Mydata.zip)
Thank you.
Thank you, Daniel Osorio for your reply. The analysis in SPIDER I have to do is of "species Monophyla".
Please see attachment (R console.jpg), this is what i got after executing command suggested in the above post. Also, in query post I have attached "Mydata.zip" the file has data in FASTA format named "Alignment.fas". This file does not possess populations but a species data, please suggest commands taking "alignment.fas" file into consideration. Wating for your reply, please keep posting.
regards,
Rahul
Hi Rahul,
The command you mentioned (head(dimnames(anoteropsis)[[1]]))is only to have a quick look at the names of the first sequence. It is not the command to build the species vector. The concept of the species vector can be a little tricky, but if you follow the tutorial, you should be ok. In your case it seems each sequence is well labelled with a consistent system starting with genus and species names separated by an underscore. Thus you can split apart each element and putting them back together (as proposed in the tutorial for the Anoteropsis dataset)
For the SPIDER dataset, we used
aa
Thank you very much! Daniel Osorio and Stephane Boyer its working...
Following the above suggestions, @ Threshold optamization step, according to BOLD (Barcode of Life Data Systems) 1% (0.01) threshold is often used as good rule of thumb, it may not always be appropriate to every dataset, and identification success can sometimes be increased if a better threshold given the data can be found. So, I have calculated threshold for my data using Taxon DNA v1.6.2, Sspecies identifier.jar, as 2.66% (0.026). This value was further used for analysis,
Command: threshOpt(gbcatdist, gbcatspp, thresh = 0.026)
is this correct. Else, suggest possible solution for optamizing threshold.
Yes you should definitely calculate the best threshold for your data if you have a dataset that allows you to do so (ideally with sequences from multiple specimens for each species). I have never used Taxon DNA v1.6.2. But we do have a function in SPIDER that does that. It is called localMinima, see page 10 of the SPIDER manual. It would be interesting to see wether you find the same threshold using different methods.
Thank you all for suggesting solution for concerned issue!
Now, I have done analysis for monophyla, as I am new to this package and even R, please help me in reteriving monophyla anaylsis done (to get output of monophyletic species in .csv format).
Even the Rosenberg analysis was done sucessfully, but how to print and retreive the tree as mentioned in tutorial (with red and grey nodes). Please keep posting.
- Badges
- Science topic
- Similar topics
- Mathematics
- Statistics
- Statistical Software
- R Statistical Package