I'm creating a massive phylogeny for my project and I am interested in partitioning the genes 16S (mitochondrial), 18S (nuclear), and 28S (nuclear) by variable and conserved regions.
I'm wondering if there is a program that can tell me this or do I eyeball it and guess?
Thank you for any help or suggestions!
Hey Samantha Ann Donohoo
My suggestion is LocARNA algorithm for aligning your sequences. the method generates a consensus secondary structure of each rDNA. The structure consists of two parts, the stem and the loop correspond to conserved and variable regions.
note: you can only align 30 taxa at each time. so to reduce the number of input taxa, you can remove the identical sequences from your matrix.
For more info click on the link below.
http://rna.informatik.uni-freiburg.de/LocARNA/Input.jsp
Cheers
Kiavash
Hi Samantha,
I recommend the freely available program PartitionFinder for determining the best-fit schemes for your genes. The program can be downloaded here: http://www.robertlanfear.com/partitionfinder/
As for partitioning them by variable region, I recommend the partitioned-data analysis program RevBayes. The program is accessible here: https://revbayes.github.io/tutorials/partition/
Also attached are the relevant literature associated with each program. Good luck!
Best,
Danny
Generally, eyeball it against good references and accept you could get it wrong.
Hell, if youre good, you can probably do it in notepad++.
Not much is going to go wrong anyway, right?