0
votes
0answers
29 views

comparing conventional phylogenetic tree to phylogenetic trees which are based on enzymes

I built trees (for 4 organisms: mouse, human, drosophila and C-elegans) for different enzymes family, compared them to the conventional tree, and try to explain them. how would you explain these ...
0
votes
3answers
67 views

Phylogenetic tree

I want to find the conventional phylogenetic tree of human, mouse, C elegans and drosophila, without all the other organisms. Do you know where can I get it? thanks, Noga
7
votes
3answers
122 views

How should I put a large phylogeny into a scientific paper?

I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is ...
1
vote
1answer
77 views

Cats, Dogs and Bears - how are they related?

What is the ancestral relationship between cats, dogs and bears? I presume they are more closely related to one another than other paraphyletic clades of mammal. Which came first? What did their ...
1
vote
1answer
135 views

Does a fully-resolved phylogenetic tree have to be dichotomous?

I read that wherever there is polytomy there is an unresolved pattern of divergence. I don't understand why this is so. When divergence takes place, is it necessary that there will be division into ...
5
votes
2answers
119 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 ...
13
votes
3answers
23k views

What is the difference between orthologs, paralogs and homologs?

These three terms are often misused in the literature. Many researchers seem to use them as synonymous. So, what is the definition of each of these terms and how do they differ from one another?