change all iqtree2 to iqtree3 (except "for older versions")

Author: trongnhanuit

doc/AliSim.md

@@ -39,7 +39,7 @@ IQ-TREE provides three matched-pairs tests of symmetry ([Naser-Khdour et al., 20
 test the two assumptions of _stationarity_ and _homogeneity_. 
 A simple analysis:
 
-	iqtree2 -s example.phy -p example.nex --symtest-only
+	iqtree3 -s example.phy -p example.nex --symtest-only
 
 will perform the three tests of symmetry on every partition of the alignment
 and print the result into a `.symtest.csv` file. `--symtest-only` option tells
@@ -83,14 +83,14 @@ stationary assumption.
 
 Now you may want to perform the phylogenetic analysis excluding all "bad" partitions by:
 
-	iqtree2 -s example.phy -p example.nex --symtest-remove-bad
+	iqtree3 -s example.phy -p example.nex --symtest-remove-bad
 
 that will remove all "bad" partitions where SymPval < 0.05 and continue the analysis with the
 remaining "good" partitions. You may then compare the trees from "all" partitions
 and from "good" only partitions to see if there is significant difference between them 
 with [tree topology tests](Advanced-Tutorial#tree-topology-tests).
 
-Other options can be seen when running `iqtree2 -h`:
+Other options can be seen when running `iqtree3 -h`:
 
 ```
 TEST OF SYMMETRY:

doc/Assessing-Phylogenetic-Assumptions.md

@@ -457,7 +457,7 @@ are very similar to each other).
 * Infer a maximum-likelihood tree for an alignment, automatically switching to CMAPLE algorithm 
   if sequence divergence is low:
 
-        iqtree2 -s data.phy --pathogen --prefix pathogen
+        iqtree3 -s data.phy --pathogen --prefix pathogen
         
 It will print two output files:
 
@@ -472,13 +472,13 @@ and remove `--pathogen` option to invoke the default IQ-TREE machinery.
 * Infer a tree like above and additionally assign branch supports using SH-aLRT test 
   with 1000 replicates using 4 CPU cores:
 
-        iqtree2 -s data.phy --pathogen --alrt 1000 -T 4 --prefix pathogen_sh_alrt
+        iqtree3 -s data.phy --pathogen --alrt 1000 -T 4 --prefix pathogen_sh_alrt
 
 The output file `pathogen_sh_alrt.treefile` will contain SH-aLRT branch supports for all internal branches.
 
 * Infer a tree like above and additionally assign SPRTA branch supports:
 
-        iqtree2 -s data.phy --pathogen-force --sprta --prefix pathogen_sprta
+        iqtree3 -s data.phy --pathogen-force --sprta --prefix pathogen_sprta
 
 The output file `pathogen_sprta.nex` will contain SPRTA branch supports for all (internal and external) branches.
 

doc/Command-Reference.md

@@ -58,15 +58,15 @@ Downloading source code
 
 Choose the source code (`zip` or `tar.gz`) of the IQ-TREE release you want to use from:
 
-<https://github.com/iqtree/iqtree2/releases>
+<https://github.com/iqtree/iqtree3/releases>
 
 For IQ-TREE version 1 please use:
 
 <https://github.com/Cibiv/IQ-TREE/releases/>
 
 Alternatively, if you have `git` installed, you can also clone the source code from GitHub with:
 
-    git clone --recursive https://github.com/iqtree/iqtree2.git
+    git clone --recursive https://github.com/iqtree/iqtree3.git
 
 For IQ-TREE version 1 please clone:
 
@@ -106,7 +106,7 @@ Compiling under Linux
 
     `j` option tells it to use all CPU cores to speed up the compilation. Without this option, `make` uses only one core, which might be slow.
 
-This creates an executable `iqtree2` (`iqtree` for version 1). It can be copied to your system search path so that IQ-TREE can be called from the Terminal simply with the command line `iqtree2`.
+This creates an executable `iqtree3` (`iqtree` for version 1). It can be copied to your system search path so that IQ-TREE can be called from the Terminal simply with the command line `iqtree3`.
 
 To compile IQ-TREE under Linux with ARM processor, use either GCC 10 (but not above), or Clang 14 or above.
 

doc/Compilation-Guide.md

@@ -347,7 +347,7 @@ If you use this model in a publication please cite:
 
 Starting with version 2.3.0, the MAST model can be executed by adding `+T` to the model option (`-m`) and providing a newick file with multiple trees by the option (`-te`). For example if one wants to fit a MAST model with different topologies contained in `trees.nwk` in conjunction with the `GTR` model to sequences in `data.fst`, one would use the following command:
 
-    iqtree2 -s data.fst -m "GTR+T" -te trees.nwk
+    iqtree3 -s data.fst -m "GTR+T" -te trees.nwk
 
 The above command will *link* GTR parameters across all the trees. That means all trees will have the same GTR model. IQ-TREE will check the number of trees inside the newick file, and then estimate the model parameters and the weights of each tree: the proportion of sites belonging to each tree.
 
@@ -359,11 +359,11 @@ An example of the newick file with 3 topologies:
 
 You can also link the GTR parameters, frequency array, and the rate-heterogeneity-across-site (RHAS) model across all the trees by including the frequency and the RHAS model in the model option (`-m`). For example:
 
-    iqtree2 -s data.fst -m "GTR+FO+G+T" -te trees.nwk
+    iqtree3 -s data.fst -m "GTR+FO+G+T" -te trees.nwk
 
 If one would like to have *unlink* components across the trees (for example, each tree has its own substitution model, frequency array and RHAS model), one can specify the unlinked components via the `TMIX` keyword in the model string. For example:
 
-    iqtree2 -s data.fst -m "TMIX{GTR+FO+G,F81+FO+R3,HKY+FO+I}+T" -te trees.nwk
+    iqtree3 -s data.fst -m "TMIX{GTR+FO+G,F81+FO+R3,HKY+FO+I}+T" -te trees.nwk
 
 The above command specifies the `GTR+FO+G` model for the first topology (inside the newick file), the `F81+FO+R3` model for the second topology, and the `HKY+FO+I` model for the third topology. These components are given in curly brackets and separated with a comma. Note that the number of components has to match with the number of topologies in the newick file.
 
@@ -388,15 +388,15 @@ Note: subst - substitution model; freq - DNA/AA frequency array; RHAS - rate het
 One can use `+TR` instead of `+T` to represent the branch-length-Restricted MAST model.
 In this model, the length of branch `x` of a tree <code>T<sub>i</sub></code> is constrained to be equal to the length of branch `y` of a tree <code>T<sub>j</sub></code> if the branches `x` and `y` split the trees <code>T<sub>i</sub></code> and <code>T<sub>j</sub></code> into the same two sets of taxa. For example:
 
-	iqtree2 -s data.fst -m "GTR+FO+G+TR" -te trees.nwk
+	iqtree3 -s data.fst -m "GTR+FO+G+TR" -te trees.nwk
 
 In the above command, all trees share the same GTR model, DNA frequencies and gamma model, and the lengths of the branches across the trees which split the taxa set into the same partition are restricted the same.
 
 **Weight-constrained MAST model**
 
 One can define a constraint array following `+T` to restrict the tree weights. The constraint array can be defined as <code>[s<sub>1</sub>,s<sub>2</sub>,...,s<sub>n</sub>]</code> where <code>s<sub>i</sub></code> can be any string. The weight of tree <code>T<sub>i</sub></code> and that of tree <code>T<sub>j</sub></code> are restricted the same value if <code>s<sub>i</sub> = s<sub>j</sub></code>. For example, assuming there are 3 topologies in the newick file:
 
-	iqtree2 -s data.fst -m "GTR+FO+G+T[x,x,y]" -te trees.nwk
+	iqtree3 -s data.fst -m "GTR+FO+G+T[x,x,y]" -te trees.nwk
 
 In the above command, all trees share the same GTR model, DNA frequencies and gamma model, and the weight of the first tree is constrained as the same as the weight of the second tree.
 

doc/Complex-Models.md

@@ -46,25 +46,25 @@ First, you need to infer a reference tree (e.g. a species tree), on which the co
 
 As an example, you can apply an [edge-linked proportional partition model](Complex-Models) with ultrafast bootstrap (1000 replicates; for comparison with concordance factors):
 
-	iqtree2 -s ALN_FILE -p PARTITION_FILE --prefix concat -B 1000 -T AUTO
+	iqtree3 -s ALN_FILE -p PARTITION_FILE --prefix concat -B 1000 -T AUTO
 
 where `ALN_FILE` and `PARTITION_FILE` are your input files. `-T AUTO` is to detect the best number of CPU cores. Here we use a prefix `concat`, so that all output files (`concat.*`) do not interfere with analyses below. If `--prefix` is omitted, all output files will be `PARTITION_FILE.*`.
 
-Moreover, IQ-TREE 2 provides a new convenient feature: if you have a directory with many (locus) alignments, you can specify this directory directly with `-p` option:
+Moreover, IQ-TREE 3 provides a new convenient feature: if you have a directory with many (locus) alignments, you can specify this directory directly with `-p` option:
 
-	iqtree2 -p ALN_DIR --prefix concat -B 1000 -T AUTO
+	iqtree3 -p ALN_DIR --prefix concat -B 1000 -T AUTO
 
 IQ-TREE detects if `-p` argument is a directory and automatically load all alignment files and concatenate them into a supermatrix for the partition analysis.
 
 
 Inferring gene/locus trees
 --------------------
 
-We now construct a set of gene/locus trees. One can manually do a for-loop, but IQ-TREE 2 provides a new convenient option `-S` to compute individual locus trees given a partition file or a directory:
+We now construct a set of gene/locus trees. One can manually do a for-loop, but IQ-TREE 3 provides a new convenient option `-S` to compute individual locus trees given a partition file or a directory:
 
-	iqtree2 -s ALN_FILE -S PARTITION_FILE --prefix loci -T AUTO
+	iqtree3 -s ALN_FILE -S PARTITION_FILE --prefix loci -T AUTO
 	# or
-	iqtree2 -S ALN_DIR --prefix loci -T AUTO
+	iqtree3 -S ALN_DIR --prefix loci -T AUTO
 
 In the second case, IQ-TREE automatically detects that `ALN_DIR` is a directory and will load all alignment files within the directory. So `-S` takes the same argument as `-p` except that it performs model selection (ModelFinder) and tree inference separately for each partition/alignment. The output files are similar to those from a partitioned analysis, except that `loci.treefile` now contains a set of trees.
 
@@ -73,7 +73,7 @@ Gene concordance factor (gCF)
 
 Given the species tree `concat.treefile` and the set of locus trees `loci.treefile` computed above, you can calculate gCF for each branch of the species tree as the fraction of decisive gene trees concordant with this branch:
 
-	iqtree2 -t concat.treefile --gcf loci.treefile --prefix concord
+	iqtree3 -t concat.treefile --gcf loci.treefile --prefix concord
 
 Note that `-t` accepts any reference tree (e.g., by coalescent/reconciliation approach) and `--gcf` accepts any set of trees (e.g. locus trees and bootstrap trees), which may contain a subset of taxa from the reference tree. IQ-Tree will write three files:
 
@@ -92,7 +92,7 @@ Site concordance factor (sCF)
 Given the species tree `concat.treefile` and the alignment, you can calculate sCF for each branch of the species tree as the fraction of decisive alignment sites supporting that branch:
 
 	# for version 2.2.2 or above
-	iqtree2 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord
+	iqtree3 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord
 	# older versions
 	iqtree2 -t concat.treefile -s ALN_FILE --scf 100 --prefix concord -T 10
 
@@ -103,14 +103,14 @@ Note that the `--scfl` option from IQ-TREE v2.2.2 will invoke model selection wi
 Instead of `-s`, you can alternatively provide a directory or a partition file. IQ-Tree then computes sCF for the concatenated alignment:
 
 	# for version 2.2.2 or above
-	iqtree2 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord
+	iqtree3 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord
 	# older versions
 	iqtree2 -t concat.treefile -p ALN_DIR --scf 100 --prefix concord -T 10
 
 Finally, you can combine gCF and sCF within a single run:
 
 	# only for the original sCF
-	iqtree2 -t concat.treefile --gcf loci.treefile -p ALN_DIR --scf 100 --prefix concord -T 10
+	iqtree3 -t concat.treefile --gcf loci.treefile -p ALN_DIR --scf 100 --prefix concord -T 10
 
 Here, each branch of `concord.cf.tree` will be assigned (or appended) with `gCF/sCF` values and `concord.cf.stat` will be written with both gCF and sCF values.
 
@@ -122,30 +122,30 @@ Putting it all together
 If you have separate alignments for each locus in a folder, then perform the following commands:
 
 	# infer a concatenation-based species tree with 1000 ultrafast bootstrap and an edge-linked partition model
-	iqtree2 -p ALN_DIR --prefix concat -B 1000 -T AUTO
+	iqtree3 -p ALN_DIR --prefix concat -B 1000 -T AUTO
 
 	# infer the locus trees
-	iqtree2 -S ALN_DIR --prefix loci -T AUTO
+	iqtree3 -S ALN_DIR --prefix loci -T AUTO
 
 	# compute gene concordance factors
-	iqtree2 -t concat.treefile --gcf loci.treefile --prefix concord
+	iqtree3 -t concat.treefile --gcf loci.treefile --prefix concord
 
 	# compute site concordance factor using likelihood with v2.2.2
-	iqtree2 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord2
+	iqtree3 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord2
 
 If you have a single concatenated alignment with a partition file that defines loci:
 
 	# infer a concatenation-based species tree with 1000 ultrafast bootstrap and an edge-linked partition model
-	iqtree2 -s ALN_FILE -p PARTITION_FILE --prefix concat -B 1000 -T AUTO
+	iqtree3 -s ALN_FILE -p PARTITION_FILE --prefix concat -B 1000 -T AUTO
 
 	# infer the locus trees
-	iqtree2 -s ALN_FILE -S PARTITION_FILE --prefix loci -T AUTO
+	iqtree3 -s ALN_FILE -S PARTITION_FILE --prefix loci -T AUTO
 
 	# compute gene concordance factors
-	iqtree2 -t concat.treefile --gcf loci.treefile --prefix concord
+	iqtree3 -t concat.treefile --gcf loci.treefile --prefix concord
 
 	# compute site concordance factor using likelihood with v2.2.2
-	iqtree2 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2
+	iqtree3 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2
 
 
 Note that you can adjust `-T 10` if you have fewer/larger CPU cores.
@@ -160,7 +160,7 @@ Specifically, because the new version of the site concordance factor uses likeli
 
 So, suppose that in the first step of the analysis you ran the command as above:
 
-	iqtree2 -s ALN_FILE -p PARTITION_FILE --prefix concat -B 1000 -T AUTO
+	iqtree3 -s ALN_FILE -p PARTITION_FILE --prefix concat -B 1000 -T AUTO
 
 That command will have figured out for you the model of evolution, all the parameters of that model, and the branch lengths of the corresponding tree. We can re-use all of that useful information in the final step. It just takes a little bit of effort to find what you need.
 
@@ -183,21 +183,21 @@ To put all of that together, we are going to change the final command of the tut
 
 	# simple command, with per-locus alignments
 	# compute site concordance factor using likelihood with v2.2.2
-	iqtree2 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord2
+	iqtree3 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord2
 
 	# simple command, with concatenated alignments
 	# compute site concordance factor using likelihood with v2.2.2
-	iqtree2 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2
+	iqtree3 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2
 
 To one of these, where we add the two extra commands via `-blfix` and `-m`, to fix all the parameters we already calculated. A reminder - do NOT use the exact commandlines above. You have to replace everything after the `-m` with what you found in your own `concat.iqtree` file:
 
 	# faster analysis, using pre-computed model parameters, with per-locus alignments
 	# compute site concordance factor using likelihood with v2.2.2
-	iqtree2 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord2 -blfix -m "Q.plant+I{0.177536}+R8{0.147295,0.0935335,0.114418,0.190578,0.108376,0.538389,0.113777,0.804005,0.0898871,1.30004,0.137297,1.95653,0.0958285,3.48597,0.0155849,6.09904}"
+	iqtree3 -te concat.treefile -p ALN_DIR --scfl 100 --prefix concord2 -blfix -m "Q.plant+I{0.177536}+R8{0.147295,0.0935335,0.114418,0.190578,0.108376,0.538389,0.113777,0.804005,0.0898871,1.30004,0.137297,1.95653,0.0958285,3.48597,0.0155849,6.09904}"
 
 	# faster analysis, using pre-computed model parameters, with concatenated alignments
 	# compute site concordance factor using likelihood with v2.2.2
-	iqtree2 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2 -blfix -m "Q.plant+I{0.177536}+R8{0.147295,0.0935335,0.114418,0.190578,0.108376,0.538389,0.113777,0.804005,0.0898871,1.30004,0.137297,1.95653,0.0958285,3.48597,0.0155849,6.09904}"
+	iqtree3 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2 -blfix -m "Q.plant+I{0.177536}+R8{0.147295,0.0935335,0.114418,0.190578,0.108376,0.538389,0.113777,0.804005,0.0898871,1.30004,0.137297,1.95653,0.0958285,3.48597,0.0155849,6.09904}"
 
 All this does is tells IQ-TREE to use the model parameters and branch lengths you already calculated. On large datasets this can save a lot of analysis time.