Making a phylogeny

Finding sequence data for your taxa

Search on Phylota
Look at Phylo. Inform. Seq. Clusters; click on "See complete taxon coverage matrix" and note which genes are sequenced for most of your species (and therefore most informative)
Go back to main taxa page if you're looking at multiple families etc. and click on Phylo. Inform. Seq. Clusters for all (at the top of the chart); click on the complete taxa coverage matrix link at the top again; click each cluster number for the genes you want to use
Download alignments > Use All > Submit; copy and paste results into a new text file; repeat for each gene into new separate files
If the alignment doesn't come up: Download cluster > Use All > Submit; copy and paste into a text file for each gene; go to MUSCLE and copy and paste the results from each download cluster into the box and submit to get the alignments
Delete undesired taxa if necessary and any duplicated species (only want one sequence per species per gene – otherwise you'll have to prune them from the tree later..)
Sequences can also be added from GenBank for other species before the MUSCLE alignment step (just copy and paste them into the text files)

Find names of fossil species in extant genera or subclades etc. in literature (need the minimum age) OR on fossilworks.org --> the age of the stratigraphic layer where the fossil was found is the approx. age
Example: Elephantulus antiquus 2.5-3.6 Ma --> 2.5 Ma minimum age for that genus (Elephantulus is an extant genus!)
Example: Rhynchocyon sp. 23-28.4 Ma --> 23 Ma minimum age for that genus

Save alignment FASTA files again with only the species name (not < or the gi number), keeping original files for cross-reference just in case
Grep in text editor --> Find: >(\w+)_(\w+)_(\w+)_(\w+) Replace: >\3_\4 Replace All
Put all of these new files in a new subfolder
Convert these FASTA files to Nexus format with GENEIOUS (export as Nexus files)...
Run Beastin R script to add placeholders for missing species, make all sequences the same length, and to help you check for repeats of species (e.g., typos)

Look up if each gene you're using is coding or non-coding on genecards.org
In Beauti: link subst. models (select all), HKY, Gamma, (1+2)3, lognormal relaxed clock (estimate), speciation: Yule, Mu's = lognormal, ucld's = Gamma, 1, 1, 1, 0; Taxa: select groups and set ages according to fossil dates; MCMC; generate the XML file for BEAST

Open Tracer
Import log file from CIPRES run
Set burnin value to the same as the run (e.g., 10,000,000); increase burnin if the distribution is weird or if things are coming up yellow or red
Re-adjust things in previous step if necessary; this is just a good visual check

Open TreeAnnotator
Burnin = 1000 (10% of total runs set previously), these are the number of initial trees that will be thrown out
Max clade credibility tree
Mean heights
Input = .trees file from CIPRES
Output = whatever name you want

Open FigTree
Import the file made from TreeAnnotator
Adjust settings as desired: Ordering > Decreasing, Scale axis (not scale bar) > Reverse