Our lab generated 763 HIV sequences that we now need to analyse through evolutionary methods, namely dN/dS. Plus, we also want to identify recombination patterns between B and F forms (possibly C?).
I'm not familiarized with the computational algorithms needed to do so. Can you guys help us solve this? Or point me in the right direction, please?
Thank you in advance.
Daniel
For aligning your sequences I recommend both PRANK or MAFFT with highest accuracy settings. DO NOT USE clustalW, it gives very bad results.
After you aligned your sequences with PRANK or MAFFT you can remove poorly aligned regions by using GUIDANCE, an alignment filtering tool developed by Tal Pupko.
This way you will get clean alignments.
Hey Daniel,
how long are your sequences? To analyze recombination patterns you can use simplot. The settings have to be adjusted to the length of the sequences you have generated.
http://sray.med.som.jhmi.edu/SCRoftware/simplot/
They are, for the first group 320 nt long and for the second ~620nt long.
Daniel,
most of the things you can do them with Mega. That is a software package, which can calculate the ratios you need. The documentation on their website is also very good. For recombination analysis you should use SimPlot and for the rest Mega. I hope that helps.
http://www.megasoftware.net/
I´ve downloaded it, kinda tricky to use though. I'm cleaning the sequences and framing them correctly now. Thank you for the help Ijad!
Hi Daniel,
take a look at the software PAML. It calculates dN/dS and may be used to estimate parameters and test hypotheses to study the evolutionary process. I hope that helps too.
Moara
For dN/dS analysis you can use several tools: PAML, HYPHY (http://www.hyphy.org/docs/GUIExamples/index.html), DataMonkey (http://www.datamonkey.org/)
For recombination, my recomendation is RDP3 (http://darwin.uvigo.es/rdp/rdp.html)
u can also try swakk sever http://oxytricha.princeton.edu/SWAKK/1DKAKS.html for dn/ds but u need a reference seq for this analysis
For aligning your sequences I recommend both PRANK or MAFFT with highest accuracy settings. DO NOT USE clustalW, it gives very bad results.
After you aligned your sequences with PRANK or MAFFT you can remove poorly aligned regions by using GUIDANCE, an alignment filtering tool developed by Tal Pupko.
This way you will get clean alignments.
Hi Daniel
What's up!!Nice that you are working with HIV!
I would recommend you to use JpHMM for recombination detection and to identify codons under selection I recommend HyPhy/datamonkey as suggested by David Peris.
Cheers
Frank
Long time no see Frank! I made contact with your former advisor and perhaps in some near future...
As of now I'm banging my head against this wall and any help is most welcome, which, by the way, requires a former thank you for your input.
Perhaps we can talk later? For more advice and for me to be updated of the position you currently hold. What forms of internet comunication you are more inclined to use nowadays?
Regards,
Daniel
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