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Synthesizing and dating phylogenies using the Open Tree of Life, SSB UNAM 2023: Jan 13, 2023
Synthesizing and dating phylogenies using the Open Tree of Life, SSB UNAM 2023
Jan 13, 2023
10 am - 2 pm
Instructors:
Mark Holder, Emily Jane McTavish, Luna Luisa Sanchez Reyes, Ben Redelings
We have borrowed the Carpentries website template and installation instructions. This is not a Carpentries workshop (although we highly recommend them!). Learn more about the carpentries at https://carpentries.org/
Synthesizing and dating phylogenies using the Open Tree of Life
The (Open Tree of Life project)[tree.opentreeoflife.org] provides an integrated set of tools and data resources to make phylogenetic knowledge more accessible across the diversity of life. Participants will learn to use the Open Tree of Life tools and data stores to evaluate and unite phylogenetic inferences to generate taxonomically complete synthetic trees, which they can apply to their individual research questions in evolutionary biology. The focus of this workshop is demonstrating new features of the Open Tree of Life’s infrastructure: services for adding dates to nodes, constructing supertrees from arbitrary sets of trees, and performing generalized conflict analyses. While most of the services and tools demonstrated require only a browser to access, some will require access via a command line. The tools are accessible via Windows, Mac, or Linux devices.
The workshop will cover using Open Tree of Life phylogenetic study curation tools to standardize the taxonomic names and metadata for published phylogenetic estimates. We will demonstrate tools to assess concordance and conflict across different phylogenetic estimates, and between phylogenetic estimates and taxonomic relationships. Using OpenTree’s custom synthesis tools, participants will generate synthetic summary trees for their taxa based on existing phylogenetic inferences. We will apply existing node date estimates to these synthetic trees, and infer date estimates for undated nodes in trees. Together these approaches will provide participants with the skill set to obtain a dated tree for taxa of interest and understand how published estimates disagree with each other with respect to those taxa.
Requirements:
Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). Run the Installation checks to make sure everything is working in advance of the workshop
Bring a recently published tree of interest to you if you can access one (newick or nexus format)
Create a Github account if you don't have one. Github.
To participate in this workshop,
you will need to be able to access Bash, Python3 and (optionally) Jupyter notebooks, and use git to clone repos.
In addition, you will need an up-to-date web browser and a text editor.
If you already have these software installed and accessible on your laptop, please skip to the bottom and run the checks.
Otherwise there are installation instructions listed below.
The Carpentries maintains a list of common issues that occur during installation as a reference for instructors
that may be useful on the
Configuration Problems and Solutions wiki page.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple
tasks more quickly.
Click on "Next" four times (two times if you've previously
installed Git). You don't need to change anything
in the Information, location, components, and start menu screens.
From the dropdown menu select "Use the nano editor by default" and click on "Next".
Ensure that "Git from the command line and also from 3rd-party software" is selected and
click on "Next". (If you don't do this Git Bash will not work properly, requiring you to
remove the Git Bash installation, re-run the installer and to select the "Git from the
command line and also from 3rd-party software" option.)
Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
Ensure that "Use Windows' default console window" is selected and click on "Next".
Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected
and click on "Next".
Click on "Install".
Click on "Finish".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
Quit command prompt by typing exit then pressing [Enter]
This will provide you with both Git and Bash in the Git Bash program.
The default shell in some versions of macOS is Bash, and
Bash is available in all versions, so no need to install anything.
You access Bash from the Terminal (found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep Terminal in your dock for this workshop.
To see if your default shell is Bash type echo $SHELL in
Terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.
The default shell is usually Bash and there is usually no need to
install anything.
To see if your default shell is Bash type echo $SHELL in
a terminal and press the enter/return key. If the message printed does
not end with '/bash' then your default is something else and you can run
Bash by typing bash.
Git
Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser.
You will need an account at github.com
for parts of the Git lesson. Basic GitHub accounts are free. We encourage
you to create a GitHub account if you don't have one already.
Please consider what personal information you'd like to reveal. For
example, you may want to review these
instructions
for keeping your email address private provided at GitHub.
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.
Text Editor
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on macOS and
Linux is usually set to Vim, which is not famous for being
intuitive. If you accidentally find yourself stuck in it, hit
the Esc key, followed by :+Q+!
(colon, lower-case 'q', exclamation mark), then hitting Return to
return to the shell.
nano is a basic editor and the default that instructors use in the workshop.
It is installed along with Git.
Others editors that you can use are
Notepad++ or
Sublime Text.
Be aware that you must
add its installation directory to your system path.
Please ask your instructor to help you do this.
nano is a basic editor and the default that instructors use in the workshop.
See the Git installation video tutorial
for an example on how to open nano.
It should be pre-installed.
Python is a popular language for
research computing, and great for general-purpose programming as
well. Installing all of its research packages individually can be
a bit difficult, so we recommend
Anaconda,
an all-in-one installer.
Regardless of how you choose to install it,
please make sure you install Python version 3.x
(e.g., 3.6 is fine).
One option for running the examples is Python using the Jupyter Notebook,
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all
supported
(some older browsers, including Internet Explorer version 9
and below, are not).
Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
Download the Anaconda Installer with Python 3 for Linux.
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
Open a terminal window and navigate to the directory where
the executable is downloaded (e.g., `cd ~/Downloads`).
Type
bash Anaconda3-
and then press
Tab to autocomplete the full file name. The name of
file you just downloaded should appear.
Press Enter.
You will follow the text-only prompts.
To move through the text, press Spacebar.
Type yes and press enter to approve the license.
Press Enter to approve the default location
for the files.
Type yes and press Enter
to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).
Close the terminal window.
Installation checks (Please complete before the workshop starts)
Git check
You should be able to open a terminal window and run:
git
This should print out some text that starts with "usage: git [--version] [--help] [-C ] [-c =]"
Jupyter check
jupyter notebook
This should open up a browser window that says "jupyter" at the top. If you click on 'new' in the upper right, there should be an option to create a python3 notebook.
(You can close this window and close the terminal.)
If theses checks work, then you are all set!
Otherwise, please follow the installation instructions above, and then try these tests again. Contact ejmctavish@ucmerced.edu if you are still having issues.