SplitsTree, an open-source project developed by the University of Tuebingen, is a versatile application offering a plethora of algorithms and tools for processing both unrooted and rooted phylogenetic trees and networks. Accessible through the following link: SplitsTree, it empowers users with a comprehensive suite of functionalities.
For local installation, users can download SplitsTree from: Download SplitsTree. Once installed, SplitsTree enables users to upload alignments or trees, providing a dendrogram-like visualization. Each input sequence is represented as a tip with a corresponding label, while inner nodes and edges connect these tips or nodes, forming the network.
In downstream analyses, users often require tasks such as coloring tips based on attributes, highlighting specific network components, or modifying label text. SplitsTree facilitates these operations through its View tab, offering options to format nodes and edges. However, manual navigation and clicking are necessary for selections.
To streamline network formatting tasks and leverage the robust capabilities of R, users can utilize the present SplitstRee R package.
This integration enhances the rendering of networks generated by SplitsTree, harnessing the full potential of the R environment.
install.library("devtools")
install_git(https://github.com/abrozzi/SplitstRee.git)
Use the tab File -> Export to export the network including mandatory fields Taxa and Network. You can select also other fields. The file format is a text file.
The exported network should look like the following:
#nexus
BEGIN Taxa;
DIMENSIONS ntax=140;
TAXLABELS
[1] '88'
[2] '89'
[3] '110'
[4] '111'
[5] '112'
;
END; [Taxa]
BEGIN Trees;
PROPERTIES rooted=yes;
[TREES]
[1] tree 't1'=[&R] (121:0.1484583917587429,(47:0.10443825927426448,105:0.10832991141364293):0.007390799743357943):0.004345286343588104,((((97:0.1123931641820975,(8:0.09844731583656807,28:0.0973001623178561):0.00916006309308222):0.005493354891964678)
END; [Trees]
BEGIN Network;
DIMENSIONS ntax=140 nvertices=278 nedges=277;
DRAW to_scale;
TRANSLATE
2 '88',
3 '86',
4 '95',
;
VERTICES
1 -0.100395784 0.0 s=n,
2 0.0 0.0 s=n,
3 0.0039716596 0.012728599 s=n,
4 0.0079152705 0.015233612 s=n,
5 0.039169874 0.021456474 s=n
;
VLABELS
2 '88' x=12 y=-74 f='Dialog-PLAIN-10',
3 '86' x=12 y=156,
4 '95' x=12 y=122,
5 '10' x=12 y=22,
;
EDGES
1 1 2 s=163 w=0.100395784,
2 142 1 s=187 w=0.0109897,
;
END; [Network]
The package provides a real example of an export file from SplitsTree:
myfile <- system.file("input.nexus", package = "SplitstRee")
To read the network inside R use:
net <- import.nexus(myfile)
I had some troubles with git push. Basically everytime I was doing a push a pop-up window saied "Username for https://github.com". Next message was to insert password, but nothing worked. Surfing a bit the web,I found the solution which worked for me.
- Open terminal and type:
ssh-keygen -t ed25519 -C "myemail@something.com"
ed25519 is an algorithm.
- Create a file:
nano ~/.ssh/config
- Insert in the file
Host github.com
AddKeysToAgent yes
UseKeychain yes
IdentityFile ~/.ssh/id_ed25519
- In the terminal
ssh-add --apple-use-keychain ~/.ssh/id_ed25519
- Finally in the project Settings tab of github.com add a Deploy Key:
cat /Users/abrozzi/.ssh/id_ed25519.pub
which is something like:
ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAILFBLSrDAAI2U21mDcSddnQjgouGfGXfr8AfQ8SQNzJb alessandro.brozzi@gmail.com
copy paste and add a title in github.com.
1 - Create by RStudio a project to build a package:
~/ab/mypack
2 - Create a repository on GitHub
3 - Move to the local package directory and:
cd ~/ab/mypack
git init
git add .
git commit -m "first commit"
git remote add origin https://github.com/ab/mypack.git
git push -u origin master
4 - In Rstudio you can do the same by Git menu: commit -> push-
5 - If you need proxy add in your home a file .Renviron with the following lines:
http_proxy="http://myproxy.net:port{.uri}"
https_proxy="https://myproxy.net:2011"