I am trying (not very successfully) to analyse some phenotypic data of bacterial populations using the above programs but have no idea where to start and am just after some advice to get me going. I have sequenced bacterial rpoB genes and conducted a number of biochemical experiments to obtain phenotypes for each isolate, however I am having some trouble looking for associations between rpoB data and phenotypes using AMOVA. Has anyone tested housekeeping genes within phenotypes/populations and can they help push me in the right direction in setting up file data for either of these programs? Cheers
Since as what I understood you have phenotypic data set and Sequence data. Am I Right? If so then you can use many programmes apart from above two like STRUCTURE; PAUP (Having Bayesian Algorithm) or MEGA 6.0.
For the combination Areliquin and GenALEX can be used to get AMOVA. To make input files use CONVERT software (This software is freely downloaded and using this you can make input files for many programmes).
GenAlex is freely available along with the tutorial which is very easy.
In case any trouble contact me
With best regards
GenAlex is very user friendly program, but nor for sequence data as I know. So, you should go for Arlequin. Moreover, as a further suggestion, you can look for NJ or upgma tree for your sequence data and interpret relationships of your different phenotypes on the tree. Good luck!
I also used Arlequin successfully for AMOVA of sequence data. GenAlex is for genetic marker data.
Cheers! Thanks everyone for your advice. Do you have any tips on a first time Arlequin user? I've had a quick look and it's not striking me as "user-friendly".
Its not so easy, but the manual is quite helpful. Moreover, the software can create you example input files with explanations (called project file) in which you just replace the examples with your data. The input file is divided in sections, depending on what you want to analyse. You always need the profile section (giving your data properties), the data section (your haplotypes) and samples section (assigning the haplotypes to populations). You may also need a Structure section, which groups the populations, so that you can perform an AMOVA to get variance among and within groups,
In the Arlequin software you have to start a new project and load your prepared project file (input file). Then you find a menue of possible analyses which you can check or un-check. Then run and the output file is created in htm format.
cheers
Hi,
I realize I am a little late with my advice, but I have struggled a lot with Arlequin, because this programm can really be a b*#+ when it comes to taking the infile...Apart from the convert program you can also use create, which is also freely available.
Sometimes it all stops dead because you are missing a space somewhere. So I am happy to send you an old infile from my work, if need be.
Good luck!
Ann-Christin
Thanks everyone for their help/advice! I'm actually glad that someone is feeling the same as me about this program ;-)
Would you be able to send me an old infile to see how everything is supposed to be set out, Ann-Christin?
no problem! I will send it today. It does sound stupid, but it maybe necessary to actually count the number of spaces and check if they are spaces or tabs.
- Badges
- Science method