Phylogenetics: SMap lab

From EEBedia
Revision as of 16:15, 6 April 2020 by Paul Lewis (Talk | contribs)

Jump to: navigation, search
Adiantum.png EEB 349: Phylogenetics
In this lab you will learn how to use the program sMap, written by Giorgio Bianchini and Patricia Sánchez-Baracaldo. sMap uses stochastic character mapping to assess correlation among discrete characters.

Download sMap

Login to Xanadu and request a machine as usual:

srun --pty -p mcbstudent --qos=mcbstudent bash

Use curl to download the tar-gzipped file sMap-linux-x64.tar.gz (note the L in -LO is important in this case because the URL involves a redirect that should be followed to get to the actual file):

curl -LO

Unpack the tar file:

tar zxvf sMap-linux-x64.tar.gz

You can now delete the tar.gz file if you want:

rm sMap-linux-x64.tar.gz

The executable file sMap is buried inside the directory created when you extracted the tar file. You can either always specify the full path to this file when you want to run it, or you can use a couple of different methods to make invoking it easier. One of the simplest methods is to create an alias:

alias smap="$HOME/sMap-linux-x64/sMap"

Now typing smap at the console, whereever you are, will invoke the program (try it!). You can see any aliases you've defined by typing alias at the command prompt.

If you want your alias to be present whenever you login to Xanadu, you need to add it to your .bashrc file. The .bashrc file is one of those files beginning with a dot that are hidden by default, so you will not see it when you type ls in your home directory. You can see if you tell the ls command that you want to see everything:

ls -la

Edit the .bashrc file (which may not even exist yet) and add (on a line by itself at the very bottom of the file) the same alias command that I specified above. This will be loaded the next time you log into Xanadu.

Downloading the data for the tutorial

Download the Pontederiaceae data for the tutorial using curl:

curl -L >