Phylogenetic methods - computer practicals
Parsimony    Maximum likelihood    Bayesian inference    Species tree    home

Department of Botany, Charles University, Prague (2021-2024)

Species tree estimation

A ZIP file with necessary software is here. Download it and unzip.
BEAST - Bayesian Evolutionary Analysis by Sampling Trees. Program for Bayesian phylogenetic analysis of molecular sequences using MCMC. Look also here.
Tracer - a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference
ASTRAL - a tool for estimating an unrooted species tree given a set of unrooted gene trees
FigTree - phylogenetic tree viewer

Other software recommended to install

• Notepad++
• Total Commander

Tasks 1 (to work with Amomum dataset) - *BEAST in BEAST2

after you are done submit the answers using this Google form
If an advice is required, contact Tomáš Fér: tomas.fer_AT_natur.cuni.cz

1. Prepare the XML input file for *BEAST using BEAUti

• open BEAUti and set the template using: File -> Template -> StarBeast

• load the alignments: File -> Import Alignment - select the two NEXUS files with ITS and matK alignments (hold Shift key when selecting)

• select 'Taxon sets' tab, click on 'Guess' and select 'split on character' and select 'and take group(s)' 1, click 'OK'. Then edit Wurfbainia to Wurfbainia1 and Wurfbainia2

• select 'Site Model' tab, select appropriate models for both loci
  Question 1: What types of base substitution models are offered in BEAUti?

  • Amomum_ITS (K2P+I): select 'Subst Model' as 'HKY', set 'Frequencies' to 'All Equal', set 'Proportion Invariant' to '0.5' and select 'estimate'

  • Amomum_matK (HKY+G): select 'Subst Model' as 'HKY', keep 'Frequencies' as 'Estimated', set 'Gamma Category Count' to 4 and 'shape' to 'estimate'

  Question 2: What dose it mean if base frequencies are equal or estimated?

• select 'Clock Model' tab, keep defaults
  Question 3: What type of clock are you selecting? What does this mean?

• select 'Multi Species Coalescent' tab, set 'ploidy' to 'autosomal_nuclear' for ITS, and 'Y or mitochondrial' for matK

• select 'priors' tab, select 'Tree.t:Species' prior to 'Yule'

• select 'MCMC' tab, select 'Chain Length' to 10000000, 'Store Every' to 5000, under 'tracelog' set 'Log Every' to 5000

• save the XML file: File -> Save As

2. Run *BEAST analysis

• open BEAST and choose File.. to select the XML file

• click Run

• wait until the analysis is finished (the message about Total calculation time and End likelihood appears)
  Question 4: What is the likelihood of the model?

3. Analyze results with Tracer

• open Tracer, click on File -> Import Trace File… and select the *.log file

• click on 'posterior' Trace on the left side and look at the statistics, distribution and sampling by clicking to 'Estimates', 'Marginal Density' and 'Trace' tabs, respectively
  Question 5: What is the ESS for 'posterior'? What ESS states for?

• select all 'TreeHeight' traces (i.e., age of the groups) by holding Shift key when selecting, look at the 'Marginal Density', try different 'Display'
  Question 6: What are the differences among trees? Which tree has the widest distribution?

• sellect 'clockRate' trace and look at the 'Estimates
  Question 7: What is the mean value and what is 95% HPD interval? What does this clockRate value mean? Is clock rate higher for ITS or for matK?

4. Summarize trees with TreeAnnotator

• open TreeAnnotator

• set 'Burnin percentage' to 10 (i.e., first 10% of trees will be removed)

• set 'Posterior probability limit' to 0 (i.e., all nodes will be annotated)

• set 'Target tree type' to Maximum clade credibility tree

• set 'Node heights' to Median heights

• Input Tree File – select the species.trees file

• Output File – name the resulting species tree (e.g., species.tre)

• click on the Run button
  Question 8: How many trees were processed?

• repeat this TreeAnnotator run with trees for ITS and matK, i.e., generate another two *.tre files with gene trees

5. View species tree with FigTree

• open the resulting species tree and look at posterior probabilities, select 'Branch Labels' to display ‘posterior’
  Question 9: What is the support value for Amomum and Lanxangia?

• look also at ITS and matK gene trees and compare them to the species tree
  Question 10: Is the topology of gene trees and the species tree different and how? How the topological differencies correlates with posterior probabilities in the species tree?

Tasks 2 (to work with Zingiberaceae dataset)

6. Create a species tree with ASTRAL

• place the input file (geneTrees.tre) to the folder with ASTRAL

• open the commandline here

• type this command
  java -jar astral.5.7.7.jar -i geneTrees.tre -o astral.tre

• open the resulting astral.tre in FigTree and re-root with Siphonochilus
  Question 11: What is the local posterior probability (LPP) for Cornukaempferia and Curcuma?

Thank you for participating in *BEAST/ASTRAL practicals...