Question: Bootstrap & p distance distribution
0
gravatar for a.alsayed.phd
16 months ago by
a.alsayed.phd10 wrote:

Dear all, Please, if I have multiple sequence alignments for parts of a virus genome; how can I end up with phylogenetic tree (circular tree) showing bootstrap & p distance on it? Also how can I plot the p distance distribution? Many Thanks in advance

ADD COMMENTlink modified 16 months ago by Kevin Blighe39k • written 16 months ago by a.alsayed.phd10
1
gravatar for Kevin Blighe
16 months ago by
Kevin Blighe39k
Republic of Ireland
Kevin Blighe39k wrote:

There is a lot of information on the World Wide Web about building phylogenetic trees, but it's all quite sparse, meaning that you'll have to piece it all together to get what you want.

This first tutorial may be of use to you in order to help you to get from your FASTA sequences to a clustering object / tree structure: Using R to Caculate Genetic Distance and Generate Phylogenetic tree. It utilises the ape package in R. NB - the typeo in the title is not my own.

Building circular dendrograms / phylogenetic trees

If you want more information on building circular dendrograms, take a look at this Biostars thread, to which I have contributed: A: how to draw circular dendrogram with distance information There are also many pages on the WWW that provide information on how to build these in various ways.

Bootstrap the tree structure

If you want to bootstrap the tree structure (dendrogram) and derive P values for the branching, then use PVclust. Again, here's a Biostars thread to which I have contributed: A: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?

P value distribution

If you want to plot the P value distributions, take a look here: DESeq2 unequal sample sizes

Finally, in order to piece all of this together in a single figure, make the use of mfrow in plot(), or the cowplot or gridExtra packages.

Hopefully this helps you somewhat.

Kevin

ADD COMMENTlink modified 16 months ago • written 16 months ago by Kevin Blighe39k

Many thanks Prof. Kevin for these information

ADD REPLYlink written 16 months ago by a.alsayed.phd10

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 16 months ago by WouterDeCoster37k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2494 users visited in the last hour