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Update documentation for CLI command renames and new commands

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Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
This commit is contained in:
Eric Coissac
2026-08-28 23:06:05 +02:00
parent 95fa0c93b2
commit caf59b5658
38 changed files with 666 additions and 2433 deletions
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doc/index.html
+5 -37
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@@ -813,34 +813,6 @@
<li class="md-nav__item">
<a href="usage/name-tree/" class="md-nav__link">
<span class="md-ellipsis">
name-tree
</span>
</a>
</li>
<li class="md-nav__item">
<a href="usage/unitig/" class="md-nav__link">
@@ -898,14 +870,14 @@
<li class="md-nav__item">
<a href="usage/reindex/" class="md-nav__link">
<a href="usage/convert/" class="md-nav__link">
<span class="md-ellipsis">
reindex
convert
@@ -1282,11 +1254,7 @@
</tr>
<tr>
<td><a href="usage/phylo/"><code>phylo</code></a></td>
<td>Compute pairwise evolutionary-distance proxies, trees, and phylogenetic exports</td>
</tr>
<tr>
<td><a href="usage/name-tree/"><code>name-tree</code></a></td>
<td>Translate a TNT/PhyG numeric-label tree export back to real taxon names</td>
<td>Compute pairwise genome distances, trees, and phylogenetic exports</td>
</tr>
<tr>
<td><a href="usage/unitig/"><code>unitig</code></a></td>
@@ -1297,8 +1265,8 @@
<td>Estimate approximate-index parameters before indexing</td>
</tr>
<tr>
<td><a href="usage/reindex/"><code>reindex</code></a></td>
<td>Convert an index's evidence representation (exact ↔ approximate)</td>
<td><a href="usage/convert/"><code>convert</code></a></td>
<td>Convert an index's evidence representation (exact/approximate/hybrid), in place</td>
</tr>
<tr>
<td><a href="usage/utils/"><code>utils</code></a></td>