Phylogenetic Tree Using Numts

Question

[rehma.ar]

dear all! i am working on a project in which i want to 1)identify numts and their location on the genome (blast mtDNA against whole genome).

2)align nuclear genome of at least 10 different breeds of same organism, genomes having common numts are closely related.

3)based on that information(numts) i want to develop a phylogenetic tree.

my question is which tool i should use to build the tree. and is there a tool that uses Markov Chain Monte Carlo(MCMC).

thanks in advance....

Answer 1

[Leonor Palmeira]

There are several tools for phylogenetic inference, I would try PhyML (maximum likelihood method) and, as you are interested in MCMC: BEAST-mcmc.

In your step (2) , I assume you want to align numts, not nuclear genomes, right?

[numts = nuclear copies of mtDNA]

[rehma.ar]

thanks for your reply. i want to align nuclear genomes, not the numts. as you can in this article, "http://mbe.oxfordjournals.org/content/26/10/2175.short" though they used it for different species but i want to use it for different breeds of same species.

two tools that you have mentioned, do you have any idea wich one is better?

[Leonor Palmeira]

In this paper, they do not build a phylogeny based on nuclear genomes, they just use an "undisputed phylogeny" from another paper (Goodman, 1998). What is your species of interest?

[rehma.ar]

i want to study the evolution of numts in pig genome.

[Leonor Palmeira]

Then, if what you want to do is reproduce this article, but on different breeds of pig, you will have to build a phylogeny of your breeds (but definitely not on the whole genome, just on some genes that evolve rapidly between breeds) and then use this as an "undisputed phylogeny".

[rehma.ar]

ok once i have the "undisputed phylogeny" only than i can study the numts. is that what you mean? or if you have seen any article on that can you plz send me the link.

[Leonor Palmeira]

I've never worked on numts, so my suggestions here are only based on what I've read in the paper you are using. You should start reading the details on this paper, this will help you clear your thoughts.

Answer 2

[rehma.ar]

to start making tree with beast i need to have a .nex file but after alignment with stampy i would have a .bam file

so how can i convert that .bam file to .nex file

[Leonor Palmeira]

Please post a new question for this.