What follows is a description of how you would set up this file from scratch. If you want to skip this step, you can just download the pre-formatted configuration file by clicking here. PartitionFinder2 gets most of its instructions from a simple configuration file called 'partition_finder.cfg'. Next we need to set up the file that tells PartitionFinder2 what kind of analysis we want to do.
GENEIOUS PRIME TUTORIALS FULL
When you click 'OK' you'll get a warning you can ignore, then an option box which asks how long the names should be in the exported file, choose the 'Relaxed Phylip - Full Length.' option, and leave the other boxes unticked. Click 'OK', then save the file in the "beetles" folder on the desktop as 'cognato.phy'. You'll get a list of options for the file format. Once you have Geneious, open up the 'cognato.nex' file, then go the 'File' menu, click 'Export', then 'Selected documents.'. And don't worry - the free version is all we need here. If you don't have Geneious, it's free and you can download it from. This section describes how do this, but if you want to skip this step, click here to dowload the phylip formatted alignment.Ĭhanging alignment formats can be a notorious pain, but luckily it's made pretty simple by Geneious. Right now, our alignment is in nexus format, so we need to convert it.
PartitionFinder2 works with phylip formatted alignments. I'm going to save the file as "cognato.nex" in a folder on the desktop called "beetles". The original data is available from DataDryad here. You can download the file we'll be using in this tutorial by clicking here. This dataset consists of a nuclear protein coding gene, a mitochondrial protein coding gene, and 16S rRNA. For instructions, turn to page 7 of the manaul for Mac/Linux systems, and page 9 for Windows systems.įor this tutorial, we'll be analysing a publicly available dataset from bark beetles (Cognato et al 2001). Then, if you haven't used PartitionFinder2 before, make sure that you can run at least one of the example datasets.
GENEIOUS PRIME TUTORIALS INSTALL
If you haven't already done so, click here to download and install PartitionFinder. If you're using Windows, you'll need to slightly modify section 4 - details are in the manual. For the purposes of this tutorial, I'll assume that you're using a Mac, and that you have PartitionFinder2 installed in your Applications folder.
GENEIOUS PRIME TUTORIALS HOW TO
It assumes you have PartitionFinder2 installed and running, you can find out how to do this in the PartitionFinder2 manual (in the 'docs' folder when you download PartitionFinder). This tutorial might help if you are unsure about any particular aspect of your analysis, or you have never thought about partitioning schemes before.
If you just want to try it out, this page isn't for you - there are much simpler quick-start instructions in the PartitionFinder2 manual. This page provides a detailed step-by-step tutorial for comparing partitioning schemes for DNA sequence alignments using PartitionFinder2.