Various Guides to Molecular Phylogenetics

By Peter Unmack

Over the years of teaching folks various aspects of conducting molecular phylogentics I've developed guides on how to do various things. This helps me to figure out how I did something in the past, as well as being helpful when training others. Hopefully you find the information to be useful too. If you find any errors, or have suggestions for improvements please email me at .

General lab advice

Various tips for organizing your samples, data and files.

Primer design guide.

Data deposition in Dryad, TreeBase and GenBank.

Data editing / datafile creation advice

Guide to chromatogram editing and sequence checking.

Guide to using Chromas and BioEdit.

Guide to data file conversion (phylip, nexus, mega, fasta).

Guide to creating haplotype datasets and tables.

Program How-tos

How to run GARLI.

How to run GARLI on CIPRES.

How to run RAxML on CIPRES.

Common PAUP analysis blocks for command line version.

How to bootstrap in TNT.

Using TreeEdit to obtain a starting tree in BEAST that is consistent with your constraints.

How to make an Arlequin input file using DnaSP.

How to phase nuclear data in DnaSP.

DNA based lab exercises

Sequence data exploration and analysis using MEGA.