Here, we’ll list helpful, additional software that you can install… but that we aren’t going to be using directly in the workshop. ## Some Useful Phylogenetics Programs
David Swofford’s PAUP* has, for decades, been one of the most popular programs for parsimony-based and (some) maximum-likelihood phylogenetic analysis. The name, PAUP*, is a recursive acronym which stands for ’* Phylogenetic Analysis Using PAUP’. You can get the most recent, command-line binary of PAUP for your system at:
http://phylosolutions.com/paup-test/
FigTree is a widely used program that visualizes phylogenies, and is particularly useful for making publication-quality figures of trees, with fine control over labeling, node rotation, scale bars, clade collapsing, etc. It does not (yet) handle trees with sampled ancestors specially, instead depicting them as regular tips attached via zero-length branches. You can get FigTree at:
http://tree.bio.ed.ac.uk/software/figtree/
RevBayes uses text files, which can be opened and editted in RStudio - which is what we’ll be doing for the workshop. However, some participants might prefer using a separate text-editor when using both RStudio and RevBayes. When you’re writing code or modifying plain-text format files, it’s nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words, auto-saving, collapsing of nested code, search that allows for regular expressions, and many other features that make Microsoft’s Notepad look like a children’s tricycle in the midst of a flock of Harvey-Davidson bikes. Some developers even prefer plain-text editors over using an IDE like RStudio, as its more ‘uncluttered’.
Some popular plain-text editors you can install on Windows are Notepad++ (a favorite of several of the organizers), Atom, or Sublime Text. nano is a basic editor that opens within the terminal, installed in Windows along with the bash-like terminal git bash when git for Windows is installed.
On Macs, two popular plain-text editors are BBEdit, Text Wrangler, Atom, or Sublime Text. The default text editor accessed through the terminal is vim, which can be difficult to use. An alternative terminal-based editor is nano, which also comes pre-installed with most macOS releases. See the Git installation video tutorial from Software Carpentry for an example on how to open nano on a macOS computer.
There are many popular plain-text editors on Linux: Gedit, Kate, Atom, or Sublime Text. For those that recently changed from Windows to Linux but enjoy Notepad++ (which is officially Windows-only), you can still use Notepad++ within a Wine Snap, or use the Linux-based look-alike, Notepadqq. nano is a basic terminal-based editor and the default that instructors use in the workshop and usually comes as part of any basic distro. vim also comes with most distros, and may be set as your default text-editor.
vim
If you ever find yourself stuck in an unnamed terminal-based text-editor that mostly just seems to show you a file’s contents, and the coordinates of where your cursor is, you have become stuck in vim. To escape, hit the Esc key, followed by :, q, ! (in other words, hit ‘colon’, ‘lower-case q’, ‘exclamation mark’, in that order), then the Return key to return to the shell.
Portions of the above text is based on text from the workshop templates supplied by [Software Carpentry] (https://carpentries.github.io/workshop-template/), which is licensed by The Carpentries organization under a CC-BY license.