I would like to make principal coordinate analysis from AFLP data somebody has a good suggestion which program to use?
Hi, Peter, you mean PCA (Principal Component Analysis) or PCoA(Principal Coordinate Analysis)? The NTSYSpc program could generate the PCoA graph but not PCA.
Hello,
I think you should try PAST. The latest version of Past, together with documentation and a link to the Past mailing list, are found at http://folk.uio.no/ohammer/past
It is really user friendly, moreover it offers many options which can be helpful to handle with binary data. Good luck.
Piotr
Hi Peter,
I use NTSYS or FAMD (http://www.famd.me.uk/famd.html). Both are user friendly.
Dear Poczai
few softwares, as aforesaid are NTSYS, DARwin, PAST etc. and another is GenALEx.
I have used NTSYS, DARwin and GenALEx. NTSYS is paid while DARwin and GenALEx are freely available online. You can use both of them, although, both are user friendly, DARwin can be more easy to use.
regards,
vikas
Peter, I agree with Piotr that PAST is the easiest and most friendly soft... You can even publish such results :) Article Genomic diversity of cercarial clones of Himasthla elongata ...
Dear Peter,
Hope all is well.
Today, there are various numbers of tools to help researchers to draw high-quality graphs according to their needs. Even though standalone tools are widely found in the literature, nevertheless, I highly recommend you to use R packages in order to design unique graphs for your proposes. The main merits of R packages are the quality of these accessories. Some libraries in R including ggfortify, cluster, etc can solve your problem easily. You can comfortably resize the length and the color of designed graphs.
Dear Peter,
If you want to give it a go in R, you can import your data as a matrix of 0s and 1s and use the prcomp() function to conduct the PCA.
If loci is a matrix with AFLP loci in columns and individuals in rows, with cells being presence (1) or absence (0) of the allele:
# The PCA, scaling all loci to have a unit variance
pca
Dear Dr. Poczai,
There are several packages to analysis PCA. However, among them, I recommend DARwin or GenALEx programs.
Best,
ALireza
There are many packages to run PCA using R. You can use ade4 package. It's simple and powerfull.
- Badges
- Science topic
- Similar topics
- Agricultural Science
- Agronomy
- Crop Science