Quick tutorial on using IQ-TREE webserver
IQ-TREE is available as a downloadable program and as an online interface (via web servers).
It is a powerful program that is built for speed! Maximum likelihood methods can consume a lot of compute power, the web interface can do robust analysis in just minutes.
It has some fantastic documentation with detailed tutorials - see here. Current manual available here.
Some key features of IQ-TREE are:
The strength of IQ-TREE is the availability of a wide variety of phylogenetic models:
Personally I like to use the web interface, it saves one less program taking up memory on your computer and is super quick!
I like to use the CIBID, Austria.
Reference for command line options are available here
Your alignment file can be .fasta.
, .phylip
, .nexus
.
Select the Sequence type
(you can keep it as Auto-detect
if you like, but this will save any issues incase it does not recognise your data correctly).
Leave the Partion file
blank
Details on subtitution models available here
If you have not already chosen your model, under Substitution model
leave it as Auto
and it will perform model selection for you.
I generally leave the FreeRate heterogeneity
and Ascertainment bias correction
options unchecked.
Bootstrap analysis
select Ultrafast
. This will perform bootstrap approximation using the UFBoot method Minh et al. 2013.
Check the box next to Create .ufboot file
and select 10,000
for Maximum iterations
. I leave Minimum correlation coefficient
as 0.99
and SH-aLRT branch test
as Yes
with 1000
# replicates. Select the check box next to Approximate Bayes test
I leave the Perturbation strength
as 0.5
and IQ-TREE stopping rule
as 100.
Enter your email and SUBMIT JOB
Either click on the Analysis
tab long the top or follow the link in the email and you will find your results. I find this server is super quick, usually seconds/minutes for a basic gene alignment with <100 sequences.
Select the box on the left hand side of your analysis and click the DOWNLOAD SELECTED JOBS
at the bottom.
You can now open the trees for editing in your fave program - mine is FigTree.
Open the file ending in .contree
to get the concensus tree. This will have the bootstrap supports (%) at the nodes.
If you open the .treefile
you will find the support nodes for the SH-aLRT support (%) / aBayes support / ultrafast bootstrap support (%).
Details on the analysis including the results from the model selection, parameters, and citations can be found in the .log
and .iqtree
files [open these files using a simple text reader such as TextEdit
for MacOS or similar].
Example of output from the .iqtree
file showing that after model selection the phylogeny was based on the TIM + F + I + G4 subsitution model. Remember for more details on these model check out details here
Work by Siobhon Egan
siobhon.egan@murdoch.edu.au