1-
I have sequences for different species of Bufo, these sequences are for two genes
control region and 12s. I am asking if i can construct one phylogenetic tree using both gene or it is better to use sequences of each gene separably.
2- I want to calculate the most recent common ancestor among my sequences using MEGA 6 but I dont know how can i do it as I dont have estimated age sample for the same sequenced region I did?
please I need help
Thanks
Hani
Hi Hani,
You can use both the genes separately for phylogenetic analysis...and also join them and use for another analysis. There are good number of studies where such analysis have been carried out.
Regarding question 1: You can combine the two sequences but only if the two topologies of the trees of each one gene alone do not contradict each other. If you combine the sequences, you might want to partitionate the sequences (if your program allows this) as both genes evolved a bit differently. This will give you better estimates.
Thanks for your reply, according your answers, I will build the mega file with the two genes in one row, As I will construct Mega file for the two genes separate and later make Mega file for both, but do you have any idea in how they will be arranged.
Trim the ends and place the 2 genes of each accession behind each other. Of course, if you have several copies per gene in one accession, this doesn't work. Then alignment them in the same way as the single genes.
You can align sequences from each gene using clustalw or using Mega, please make sure the order of the sequences are consistent for each gene. Export the aligned sequences as fasta format, Then use Gblocks to concatenate the two files together and generate one no gap alignment for phylogenetic tree construction. Hope it helps.
Are the two genes known to be linked, i.e. located tightly together within the same chromosome? If yes, treat them as different partitions having different substitution models and rates, concatenate them and construct the phylogeny for this particular linkage group (does not equal the species phylogeny). If no, conduct a multispecies coalescent analysis, where the two gene trees and the species tree (i.e. the "combined" tree) are estimated simultaneously.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics