Tagged Questions

4
votes
1answer
38 views

How to get smallest subtree containing a set of nodes from BioPhylo?

I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and ...
7
votes
2answers
276 views

Use of amino-acid sequences versus use of nucleotide sequences in phylogenetic analysis

Reading a paper about gene evolution, I see that they do phylogenetic analysis for bacteria using protein sequences. They take the method from another paper. I can suspect that amino-acid sequences ...
2
votes
1answer
68 views

How to build S16 rRNAs phylogenetic trees?

Here is what I know so far: Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al.[1] it is enough to select the most similar ones. There are stem regions in the ...
6
votes
2answers
91 views

phylogenetic analysis of gene enrichment?

Are there any tools to do phylogenetic analysis of gene enrichment? This is, I have a list of genes from an experiment performed in several species, with a z-score that can be described as ...
8
votes
5answers
191 views

Finding and Comparing Homologous Genes

I have a gene of of interest that I would like to compare between homologues. How does one go about finding a gene from known coding sequences across phyla? Afterwards I imagine I could do a Clustal ...
8
votes
2answers
752 views

How can rooted and unrooted (phylogenetic) trees be distinguished from one another

I understand that both are similar in structure But how can they be easily identified as one or the other? Is it simply based on the presence or lack of a named root (the root is identified as a ...