About

Here is a site for the PyPHLAWD package. There are installation and run instructions available here. Other analyses are also described as the scripts can do several analyses other than the typical runs.

News and updates

• Mar 11, 2019

  Python 3

  PyPHLAWD has now officially moved to Python 3. This means that if you were previously using the python 2 version, you can still do that but if you update (git pull or download a new copy) it will need Python 3. The library requirements are the same you will just need Python 3 versions (which means that you will probably install with pip3 install clint and so on). If you note any bugs or issues, please post them on github.

• Sep 17, 2018

  PyPHLAWD publication

  PyPHLAWD now has a publication in Methods in Ecology and Evolution that you can get here. The doi is 10.1111/2041‐210X.13096.

• Jun 5, 2018

  Adding outgroups

  We have added the ability to add outgroups to the alignments that you construct. There are more instructions in the other page. Check it out and send along any feedback as you like!

• May 25, 2018

  Another big push for enhancements

  There will be another big push for adding analyses and enhancements to input and output coming up (details here). If you have any requests, throw then into issues and on labels, put enhancements or note it in the text. I will associate it with the big push 2 project and things will start to get incorporated.

• May 10, 2018

  Prebuilt databases added

  While you can always build your own GenBank databases (with phlawd_db_maker). There are some prebuilt databases that have been added here. They are big files, so beware! But they can save you a bit of time making your own (or compiling phlawd_db_maker).

• May 9, 2018

  Examples added

  Along with several other updates, there have been two examples, one baited and one clustering that have been added. You can find the baited example here and the clustering example here. You can find more details about how to conduct runs on the run page.

• Apr 16, 2018

  More instructions

  Several things have been added to the installation, runs, and scripts. More is being added every few days.

  One notable addition is that in the installation section, we have added some instructions to using virtualenv that can be helpful for clusters and other systems where you don’t want to mess with the standard python system.

• Feb 12, 2018

  More text added

  In an effort to move away from the README instructions I have started some pages here. More will be added soon, but I have started the transfer of the information from the README.md. Slowly more will be added. Please be sure to use the issues bit to put any problems you are having.

• Jan 23, 2018

  News and updates

  PyPHLAWD has seen a bunch of development without a lot of description of how to do different kinds of runs, parameters that are worth changing, what are all those other scripts in the src directory, or other features that are coming. That is changing shortly as development has started up again. So stayed tuned for some pages to show up here that will have details about how to use the features that are already present.