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comparison iqtree.xml @ 17:4e7fd03b0a13 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit bfeaaf8691c2f88d4f6d888b4e739207afde1970
author iuc
date Thu, 20 Feb 2025 20:11:25 +0000
parents 8a15b044f890
children 09961138fcaf
comparison
equal deleted inserted replaced
16:8a15b044f890 17:4e7fd03b0a13
886 </tests> 886 </tests>
887 <help><![CDATA[ 887 <help><![CDATA[
888 IQ-TREE 888 IQ-TREE
889 ======= 889 =======
890 890
891 The full documentation can be found here_.
892
893 .. _here : http://www.iqtree.org/doc/
894
895 General Tutorial 891 General Tutorial
896 =================== 892 ===================
897 893
898 Input data 894 Input data
899 ---------- 895 ----------
939 935
940 936
941 Running example 937 Running example
942 --------------------- 938 ---------------------
943 939
944 From the download_ there is an example alignment called `example.phy` 940 From the downloads there is an example alignment called `example.phy`
945 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals. 941 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals.
946
947 .. _download: http://www.iqtree.org/#download
948 942
949 You can now start to reconstruct a maximum-likelihood tree 943 You can now start to reconstruct a maximum-likelihood tree
950 from this alignment by entering (assuming that you are now in the same folder with `example.phy`): 944 from this alignment by entering (assuming that you are now in the same folder with `example.phy`):
951 945
952 ::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc --ufboot 2000 946 ::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc --ufboot 2000
1022 This makes sense as the mammals (**Human** to **Opossum**) form a clade, whereas the reptiles **Turtle** to **Crocodile**) and **Bird** form a separate sister clade. Here the tree is drawn at the *outgroup* Lungfish which is more accient than other species in this example. However, please note that IQ-TREE always produces an **unrooted tree** as it knows nothing about this biological background; IQ-TREE simply draws the tree this way as **LngfishAu** is the first sequence occuring in the alignment. 1016 This makes sense as the mammals (**Human** to **Opossum**) form a clade, whereas the reptiles **Turtle** to **Crocodile**) and **Bird** form a separate sister clade. Here the tree is drawn at the *outgroup* Lungfish which is more accient than other species in this example. However, please note that IQ-TREE always produces an **unrooted tree** as it knows nothing about this biological background; IQ-TREE simply draws the tree this way as **LngfishAu** is the first sequence occuring in the alignment.
1023 1017
1024 Choosing the right substitution model 1018 Choosing the right substitution model
1025 ------------------------------------- 1019 -------------------------------------
1026 1020
1027 IQ-TREE will choose the best model for you automatically if specify any of the TEST models, but valid custom models can also be specified that conform to those found in Models_ page. 1021 IQ-TREE will choose the best model for you automatically if specify any of the TEST models, but valid custom models can also be specified that conform to those found in Models page.
1028 1022
1029 .. _Models: http://www.iqtree.org/doc/Substitution-Models#binary-and-morphological-models
1030 1023
1031 1024
1032 ------------------------------ 1025 ------------------------------
1033 1026
1034 Advanced Parameter Selection 1027 Advanced Parameter Selection