- + + + + + Note: Only TEST and custom models that do not rely on MF can be used in conjunction with bootstrap parameters (-b)

-IQ-TREE also works for codon, binary and morphogical data. +IQ-TREE also works for codon, binary and morphological data. @@ -769,7 +774,6 @@ - @@ -803,7 +807,6 @@ - @@ -928,9 +931,8 @@ --------------------- From the download_ there is an example alignment called `example.phy` -in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals (Source: `Phylogenetic Handbook`_) +in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals. -.. _`Phylogenetic Handbook` : http://www.kuleuven.be/aidslab/phylogenybook/home.html)). .. _download: http://www.iqtree.org/#download You can now start to reconstruct a maximum-likelihood tree @@ -1058,9 +1060,9 @@ * **example.phy.splits**: support values in percentage for all splits (bipartitions), computed as the occurence frequencies in the bootstrap trees. This file is in "star-dot" format. -* **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program SplitsTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree. +* **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program IcyTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree. -.. _SplitsTree: http://www.splitstree.org +.. _IcyTree: https://icytree.org Reducing impact of severe model violations with UFBoot diff -r 9b892d7f82cc -r 24d024316465 iqtree_macros.xml --- a/iqtree_macros.xml Sat Nov 27 09:45:09 2021 +0000 +++ b/iqtree_macros.xml Tue Apr 09 05:10:40 2024 +0000 @@ -8,6 +8,12 @@ + + + iqtree + + +

TESTONLY