diff --git a/tools/iqtree/iqtree.xml b/tools/iqtree/iqtree.xml
index 98cbaa6d283..4801e6b6507 100644
--- a/tools/iqtree/iqtree.xml
+++ b/tools/iqtree/iqtree.xml
@@ -7,6 +7,9 @@
     <expand macro="requirements"/>
     <version_command><![CDATA[iqtree3 --version 2>&1 | head -1]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
+#if $bootstrap_parameters.ultrafast_bootstrap.skip_bootstrap_for_small_alignments and $general_options.s and $general_options.s.ext == 'fasta'
+    n_unique=\$(awk '/^>/{if(seq!="")print seq; seq=""; next}{seq=seq \$0}END{if(seq!="")print seq}' '$general_options.s' | sort -u | wc -l) &&
+#end if
 iqtree3
     --prefix PREF
     #if $general_options.short_alignments:
@@ -308,7 +311,11 @@ $tree_parameters.tree_topology.test_au
 #end if
 
 #if str($bootstrap_parameters.ultrafast_bootstrap.ufboot) != ''
-    --ufboot '$bootstrap_parameters.ultrafast_bootstrap.ufboot'
+    #if $bootstrap_parameters.ultrafast_bootstrap.skip_bootstrap_for_small_alignments and $general_options.s and $general_options.s.ext == 'fasta'
+        \$( [ "\$n_unique" -ge 4 ] 2>/dev/null && echo "--ufboot '$bootstrap_parameters.ultrafast_bootstrap.ufboot'" )
+    #else
+        --ufboot '$bootstrap_parameters.ultrafast_bootstrap.ufboot'
+    #end if
 #end if
 
 #if str($bootstrap_parameters.ultrafast_bootstrap.ufjack) != ''
@@ -434,7 +441,7 @@ Note that --seqtype CODON is always necessary when using codon models and you al
         <section name="modelling_parameters" title="Modelling Parameters">
             <section name="automatic_model" expanded="False" title="Automatic model selection">
                 <conditional name="cond_model">
-                    <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See http://www.iqtree.org/doc/Substitution-Models">
+                    <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See https://iqtree.github.io/doc/Substitution-Models">
                         <option value="true" selected="True">Yes, I want to use a custom model</option>
                         <option value="false">No, a custom model is not needed</option>
                     </param>
@@ -474,7 +481,7 @@ IQ-TREE also works for codon, binary and morphological data.
                             <option value="MF">Extended model selection with FreeRate heterogeneity</option>
                             <option value="MFP">Extended model selection followed by tree inference</option>
                         </param>
-                        <param name="additional_models" type="text" optional="true" label="Additional model specifications" help="See http://www.iqtree.org/doc/Substitution-Models">
+                        <param name="additional_models" type="text" optional="true" label="Additional model specifications" help="See https://iqtree.github.io/doc/Substitution-Models">
                             <expand macro="sanitize_query"/>
                         </param>
                     </when>
@@ -672,6 +679,7 @@ IQ-TREE also works for codon, binary and morphological data.
                     </sanitizer>
                 </param>
                 <param argument="--bnni" type="boolean" truevalue="--bnni" falsevalue="" checked="false" label="Perform an additional step to further optimize UFBoot trees by nearest neighbor interchange (NNI) based directly on bootstrap alignments" help="This option is recommended in the presence of severe model violations. It increases computing time by 2-fold but reduces the risk of overestimating branch supports due to severe model violations. Introduced in IQ-TREE 1.6."/>
+                <param name="skip_bootstrap_for_small_alignments" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Skip ultrafast bootstrap for small alignments" help="IQ-TREE requires at least 4 distinct sequences to run ultrafast bootstrap (--ufboot). By default, IQ-TREE will error out when this threshold is not met. Enable this option to silently skip --ufboot when the input FASTA has fewer than 4 distinct sequences, which is useful when mapping over collections of alignments that may include small ones. Only applies to FASTA inputs."/>
             </section>
             <section name="nonparametric_bootstrap" expanded="False" title="Nonparametric bootstrap">
                 <param argument="--boot" type="integer" optional="true" label="Replicates for bootstrap + ML tree + consensus tree" help="This will perform both bootstrap and analysis on original alignment and provide a consensus tree."/>
@@ -1070,6 +1078,29 @@ IQ-TREE also works for codon, binary and morphological data.
                 <has_text text="--con-tree"/>
             </assert_command>
         </test>
+        <test expect_num_outputs="6">
+            <!-- skip_bootstrap_for_small_alignments: 3 identical sequences, ufboot should be skipped at runtime -->
+            <section name="general_options">
+                <param name="s" value="three_seqs.fasta" ftype="fasta"/>
+            </section>
+            <section name="bootstrap_parameters">
+                <section name="ultrafast_bootstrap">
+                    <param name="ufboot" value="1000"/>
+                    <param name="skip_bootstrap_for_small_alignments" value="true"/>
+                </section>
+            </section>
+            <output name="iqtree">
+                <assert_contents>
+                    <has_text text="IQ-TREE"/>
+                </assert_contents>
+            </output>
+            <output name="treefile">
+                <assert_contents>
+                    <has_text text="("/>
+                    <has_text text=";"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 IQ-TREE
@@ -1128,7 +1159,7 @@ 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`_)
 
 .. _`Phylogenetic Handbook` : https://doi.org/10.1017/CBO9780511819049
-.. _download: http://www.iqtree.org/#download
+.. _download: https://iqtree.github.io/doc/
 
 You can now start to reconstruct a maximum-likelihood tree
 from this alignment by entering (assuming that you are now in the same folder with `example.phy`):
diff --git a/tools/iqtree/iqtree_macros.xml b/tools/iqtree/iqtree_macros.xml
index be65e37749f..f268634c32e 100644
--- a/tools/iqtree/iqtree_macros.xml
+++ b/tools/iqtree/iqtree_macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.1.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">25.0</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/iqtree/test-data/three_seqs.fasta b/tools/iqtree/test-data/three_seqs.fasta
new file mode 100644
index 00000000000..d194f6cd5b0
--- /dev/null
+++ b/tools/iqtree/test-data/three_seqs.fasta
@@ -0,0 +1,6 @@
+>seq1
+ACGTACGTAC
+>seq2
+ACGTACGTAC
+>seq3
+ACGTACGTAC