Question: Phylogenies: Is PAUP compatible with ETE 3?
0
gravatar for joreamayarom
2.5 years ago by
joreamayarom110
USA/Cambridge
joreamayarom110 wrote:

I have just produced a NJ tree using PAUP and a piece of code that looks like this(Which Software Can Be Used To Build Nj Tree With Gtr+I+G Model?, my main reason to use PAUP is explained in the same post). PAUP capabilities to plot trees are relatively limited and since it stores the trees in *.tre format by default, is there a way to export my output trees in a different format like Newick, or one that is fully compatible with ETE 3 and other programs used to visualize trees?

trees paup phylogenies • 762 views
ADD COMMENTlink modified 2.5 years ago by Brice Sarver2.6k • written 2.5 years ago by joreamayarom110
0
gravatar for Brice Sarver
2.5 years ago by
Brice Sarver2.6k
United States
Brice Sarver2.6k wrote:

There are two (major) formats in which trees are stored: Newick/New Hampshire/parenthetical and NEXUS. Confusingly, both can use the .tre extension. Because PAUP* and other programs exclusively use NEXUS and others use Newick, there are a lot of ways to convert between them. You can write your own in a variety of languages. Here's a quick, three-line snippet in R:

library(ape)
a <- read.nexus("your_tree.nex")
#can be used to write any object of class 'phylo' or 'multiphylo'
write.tree(a, file="your_tree.phy")

#and, for reference, to write in NEXUS:
write.nexus(a, file="your_tree.nex")
ADD COMMENTlink written 2.5 years ago by Brice Sarver2.6k
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: 1033 users visited in the last hour