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‎doc/Assessing-Phylogenetic-Assumptions.md‎

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---
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layout: userdoc
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title: "Assessing Phylogenetic Assumptions"
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author: M Bui
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date: 2021-03-11
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author: Minh Bui
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date: 2021-03-15
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docid: 5
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icon: info-circle
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doctype: tutorial
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tags:
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- tutorial
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description: This guide is about evaluating the suitability of the data for phylogenetic analysis.
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sections:
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- name: Tests of symmetry
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url: tests-of-symmetry
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- name: Likelihood mapping
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url: likelihood-mapping
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---
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Assessing phylogenetic assumptions
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==================================
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It is important to know that phylogenetic models rely on various simplifying assumptions to
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ease computations. If your data severely violate these assumptions, it might
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cause bias in phylogenetic estimates of tree topologies and other model
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This document shows several ways to check some of these assumptions that you
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should perform before doing phylogenetic analysis.
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Likelihood mapping analysis
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---------------------------
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<div class="hline"></div>
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Likelihood mapping ([Strimmer and von Haeseler, 1997]) is a visualisation method
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to display the phylogenetic information of an alignment. It visualises the _treelikeness_
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of all quartets in a single triangular graph and therefore renders a quick
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interpretation of the phylogenetic content.
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A simple likelihood mapping analysis can be conducted with:
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iqtree -s example.phy -lmap 2000 -n 0
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where `-lmap` option specify the number of quartets of taxa that will be drawn randomly
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from the alignment. `-n 0` tells IQ-TREE to stop the analysis right after running the
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likelihood mapping. IQ-TREE will print the result in the `.iqtree` report file as well
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as the likelihood mapping plot `.lmap.svg` (in SVG format) and `.lmap.eps` file (in EPS
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figure format).
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You can now view the likelihood mapping plot file `example.phy.lmap.svg`, which looks like this:
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![Likelihood mapping plot.](images/example.phy.lmap.pdf)
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It shows phylogenetic information of the alignment `example.phy`.
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* Top sub-figure: distribution of quartets depicted by dots on the likelihood mapping plot.
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* Left sub-figure: percentages of quartets falling in each of the three areas. The
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three areas show support for one of the different groupings like (a,b)-(c,d).
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* Right sub-figure: percentages of quartets falling in each of the seven areas.
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Quartets falling into the three corners are informative and called fully-resolved quartets.
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Those in three rectangles are partly informative (partly resolved quartets) and those in the center are uninformative
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(unresolved quartets). A good data set should have high number of fully resolved quartets
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and low number of unresolved quartets.
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The meanings can also be found in the `LIKELIHOOD MAPPING STATISTICS` section of the report file `example.phy.iqtree`:
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LIKELIHOOD MAPPING STATISTICS
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-----------------------------
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(a,b)-(c,d) (a,b)-(c,d)
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/\ /\
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/ \ / \
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/ \ / 1 \
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/ a1 \ / \ / \
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/\ /\ / \/ \
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/ \ / \ / /\ \
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/ \ / \ / 6 / \ 4 \
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/ \/ \ /\ / 7 \ /\
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/ | \ / \ /______\ / \
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/ a3 | a2 \ / 3 | 5 | 2 \
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/__________|_________\ /_____|________|_____\
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(a,d)-(b,c) (a,c)-(b,d) (a,d)-(b,c) (a,c)-(b,d)
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Division of the likelihood mapping plots into 3 or 7 areas.
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On the left the areas show support for one of the different groupings
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like (a,b|c,d).
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On the right the right quartets falling into the areas 1, 2 and 3 are
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informative. Those in the rectangles 4, 5 and 6 are partly informative
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and those in the center (7) are not informative.
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.....
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The [command reference](Command-Reference#likelihood-mapping-analysis) will provide
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more options and how to perform 2-, 3-, or 4-cluster likelihood mapping analysis.
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Tests of symmetry
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-----------------
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IQ-TREE provides three matched-pairs tests of symmetry ([Naser-Khdour et al., 2019]) to
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test the three assumptions of stationarity, reversibility and homogeneity (SRH).
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test the two assumptions of stationarity and homogeneity (SRH).
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A simple analysis:
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iqtree2 -s example.phy -p example.nex --symtest-only
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iqtree2 -s example.phy -p example.nex --symtest-remove-bad
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that will remove all "bad" partitions with SymPval < 0.05 and continue the analysis with the
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that will remove all "bad" partitions where SymPval < 0.05 and continue the analysis with the
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remaining "good" partitions. You may then compare the trees from "all" partitions
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and from "good" only partitions to see if there is significant difference between them
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with [tree topology tests](Advanced-Tutorial#tree-topology-tests).
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```
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Likelihood mapping
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------------------
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<div class="hline"></div>
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Likelihood mapping ([Strimmer and von Haeseler, 1997]) is a visualisation method
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to display the phylogenetic information of an alignment. It visualises the _treelikeness_
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of all quartets in a single triangular graph and therefore renders a quick
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interpretation of the phylogenetic content.
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A simple likelihood mapping analysis can be conducted with:
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iqtree -s example.phy -lmap 2000 -n 0
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where `-lmap` option specify the number of quartets of taxa that will be drawn randomly
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from the alignment. `-n 0` tells IQ-TREE to stop the analysis right after running the
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likelihood mapping. IQ-TREE will print the result in the `.iqtree` report file as well
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as the likelihood mapping plot `.lmap.svg` (in SVG format) and `.lmap.eps` file (in EPS
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figure format).
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You can now view the likelihood mapping plot file `example.phy.lmap.svg`, which looks like this:
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![Likelihood mapping plot.](images/example.phy.lmap.pdf)
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It shows phylogenetic information of the alignment `example.phy`.
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* Top sub-figure: distribution of quartets depicted by dots on the likelihood mapping plot.
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* Left sub-figure: percentages of quartets falling in each of the three areas. The
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three areas show support for one of the different groupings like (a,b)-(c,d).
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* Right sub-figure: percentages of quartets falling in each of the seven areas.
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Quartets falling into the three corners are informative and called fully-resolved quartets.
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Those in three rectangles are partly informative (partly resolved quartets) and those in the center are uninformative
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(unresolved quartets). A good data set should have high number of fully resolved quartets
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and low number of unresolved quartets.
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The meanings can also be found in the `LIKELIHOOD MAPPING STATISTICS` section of the report file `example.phy.iqtree`:
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LIKELIHOOD MAPPING STATISTICS
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-----------------------------
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(a,b)-(c,d) (a,b)-(c,d)
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/\ /\
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/ \ / \
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/ \ / 1 \
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/ a1 \ / \ / \
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/\ /\ / \/ \
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/ \ / \ / /\ \
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/ \ / \ / 6 / \ 4 \
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/ \/ \ /\ / 7 \ /\
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/ | \ / \ /______\ / \
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/ a3 | a2 \ / 3 | 5 | 2 \
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/__________|_________\ /_____|________|_____\
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(a,d)-(b,c) (a,c)-(b,d) (a,d)-(b,c) (a,c)-(b,d)
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Division of the likelihood mapping plots into 3 or 7 areas.
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On the left the areas show support for one of the different groupings
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like (a,b|c,d).
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On the right the right quartets falling into the areas 1, 2 and 3 are
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informative. Those in the rectangles 4, 5 and 6 are partly informative
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and those in the center (7) are not informative.
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.....
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The [command reference](Command-Reference#likelihood-mapping-analysis) will provide
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more options and how to perform 2-, 3-, or 4-cluster likelihood mapping analysis.
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[Strimmer and von Haeseler, 1997]: http://www.pnas.org/content/94/13/6815.long
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[Naser-Khdour et al., 2019]: https://doi.org/10.1093/gbe/evz193
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‎doc/Command-Reference.md‎

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layout: userdoc
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title: "Command Reference"
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author: Diep Thi Hoang, Dominik Schrempf, Heiko Schmidt, Jana Trifinopoulos, M Bui, Minh Bui
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date: 2020-04-24
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docid: 8
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date: 2021-03-11
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docid: 19
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icon: book
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doctype: tutorial
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doctype: manual
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tags:
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- manual
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description: Commprehensive documentation of command-line options.

‎doc/Concordance-Factor.md‎

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layout: userdoc
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title: "Concordance Factor"
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author: M Bui
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date: 2020-05-08
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date: 2021-03-11
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docid: 6
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icon: info-circle
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doctype: tutorial

‎doc/Dating.md‎

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layout: userdoc
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title: "Phylogenetic Dating"
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author: M Bui, Rob Lanfear
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date: 2020-06-03
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date: 2021-03-11
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docid: 7
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icon: info-circle
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doctype: tutorial

‎doc/Front.md‎

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---
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layout: userdoc
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title: |
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IQ-TREE version 2.0: Tutorials and Manual
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IQ-TREE version 2.1.2: Tutorials and Manual
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Phylogenomic software by maximum likelihood
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subtitle: "<http://www.iqtree.org>"
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author: Bui Quang Minh, Jana Trifinopoulos, Dominik Schrempf, Heiko A. Schmidt
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date: April 27, 2020
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author: |
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Bui Quang Minh, Rob Lanfear,\
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Jana Trifinopoulos, Dominik Schrempf, Heiko A. Schmidt
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date: March 15, 2021
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keywords: [phylogenomic inference, maximum likelihood]
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toc: true
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papersize: A4

‎doc/convertwiki.sh‎

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let file_changed++
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AUTHOR=`git log $f | grep Author: | sed 's/.* <//' | sed 's/@.*//' | sed 's/\./ /g' | sort | uniq | tr '\n' ',' | sed 's/,$//' | sed 's/,/, /g' | awk '{for(i=1;i<=NF;i++){ $i=toupper(substr($i,1,1)) substr($i,2) }}1'`
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AUTHOR=`git log $f | grep Author: | sed 's/m.bui@anu/minh.bui@anu/' | sed 's/.* <//' | sed 's/@.*//' | sed 's/\./ /g' | sort | uniq | tr '\n' ',' | sed 's/,$//' | sed 's/,/, /g' | awk '{for(i=1;i<=NF;i++){ $i=toupper(substr($i,1,1)) substr($i,2) }}1'`
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DATE=`git log --date=short $f | grep Date: | head -n 1 | sed 's/Date://'`
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sed "s/_AUTHOR_/$AUTHOR/" $f | sed "s/_DATE_/$DATE/" | sed 's/\.\.\//\.\.\/doc\//g' > $destf

‎doc/iqtree-doc.pdf‎

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