Remove references to Nextalign CLI

Nextalign CLI was removed in Nextclade V3¹

¹ https://docs.nextstrain.org/projects/nextclade/en/stable/user/migration-v3.html#nextalign-cli-is-removed

src/index.rst

@@ -82,7 +82,6 @@ team and other Nextstrain users provide assistance.  For private inquiries,
     Auspice <https://docs.nextstrain.org/projects/auspice/>
     Nextstrain CLI <https://docs.nextstrain.org/projects/cli/>
     Nextclade CLI <https://docs.nextstrain.org/projects/nextclade/page/user/nextclade-cli/index.html>
-    Nextalign CLI <https://docs.nextstrain.org/projects/nextclade/page/user/nextalign-cli.html>
     nextstrain.org <https://docs.nextstrain.org/projects/nextstrain-dot-org/>
 
 .. toctree::

src/learn/parts.rst

@@ -236,11 +236,10 @@ together all of the above to provide a consistent way to run pathogen workflows,
 access Nextstrain tools like Augur and Auspice across computing environments
 such as Docker, Conda, and AWS Batch, and publish datasets to nextstrain.org.
 
-:doc:`Nextclade <nextclade:index>` is a web application and two command-line
-programs (``nextclade`` and ``nextalign``) for performing viral genome
-alignment, mutation calling, clade assignment, quality checks, and phylogenetic
-placement.  Nextclade can be used indepedently of other Nextstrain tools as
-well as integrated into workflows.
+:doc:`Nextclade <nextclade:index>` is a web application and a command-line
+tool for performing viral genome alignment, mutation calling, clade assignment,
+quality checks, and phylogenetic placement. Nextclade can be used independently
+of other Nextstrain tools as well as integrated into workflows.
 
 With this overview, you'll be better prepared to :doc:`install Nextstrain
 </install>` and :doc:`run a workflow </tutorials/running-a-workflow>` or :doc:`contribute

src/snippets/ambient-setup.rst

@@ -10,7 +10,7 @@
 
       conda install --override-channels --strict-channel-priority \
             -c conda-forge -c bioconda --yes \
-            augur auspice nextalign nextclade \
+            augur auspice nextclade \
             snakemake git epiweeks pangolin pangolearn \
             ncbi-datasets-cli