Reverted TOC

README.md

@@ -12,47 +12,29 @@ Foldseek enables fast and sensitive comparisons of large protein structure sets.
 [Kim W, Mirdita M, Levy Karin E, Gilchrist CLM, Schweke H, Söding J, Levy E, and Steinegger M. Rapid and Sensitive Protein Complex Alignment with Foldseek-Multimer. bioRxiv, doi:10.1101/2024.04.14.589414 (2024)](https://www.biorxiv.org/content/10.1101/2024.04.14.589414v1)
 
 # Table of Contents
-
+<!-- no toc -->
 - [Foldseek](#foldseek)
-  - [Publications](#publications)
-- [Table of Contents](#table-of-contents)
-  - [Webserver](#webserver)
-  - [Installation](#installation)
-  - [Memory requirements](#memory-requirements)
-  - [Tutorial Video](#tutorial-video)
-  - [Documentation](#documentation)
-  - [Quick start](#quick-start)
-    - [Search](#search)
-      - [Output Search](#output-search)
-        - [Tab-separated](#tab-separated)
-        - [Superpositioned Cα only PDB files](#superpositioned-cα-only-pdb-files)
-        - [Interactive HTML](#interactive-html)
-      - [Important search parameters](#important-search-parameters)
-      - [Alignment Mode](#alignment-mode)
-      - [Structure search from FASTA input](#structure-search-from-fasta-input)
-    - [Databases](#databases)
-      - [Create custom databases and indexes](#create-custom-databases-and-indexes)
-    - [Cluster](#cluster)
-      - [Output Cluster](#output-cluster)
-        - [Tab-separated cluster](#tab-separated-cluster)
-        - [Representative fasta](#representative-fasta)
-        - [All member fasta](#all-member-fasta)
-      - [Important cluster parameters](#important-cluster-parameters)
-    - [Multimersearch](#multimersearch)
-      - [Using Multimersearch](#using-multimersearch)
-      - [Multimer Search Output](#multimer-search-output)
-        - [Tab-separated-complex](#tab-separated-complex)
-        - [Complex Report](#complex-report)
-    - [Multimercluster](#multimercluster)
-      - [Output MultimerCluster](#output-multimercluster)
-        - [Tab-separated multimercluster](#tab-separated-multimercluster)
-        - [Representative multimer fasta](#representative-multimer-fasta)
-        - [Filtered search result](#filtered-search-result)
-      - [Important multimer cluster parameters](#important-multimer-cluster-parameters)
-  - [Main Modules](#main-modules)
-  - [Examples](#examples)
-    - [Rescore aligments using TMscore](#rescore-aligments-using-tmscore)
-    - [Query centered multiple sequence alignment](#query-centered-multiple-sequence-alignment)
+- [Webserver](#webserver)
+- [Installation](#installation)
+- [Memory requirements](#memory-requirements)
+- [Tutorial Video](#tutorial-video)
+- [Documentation](#documentation)
+- [Quick Start](#quick-start)
+  - [Search](#search)
+    - [Output](#output-search)
+    - [Important Parameters](#important-search-parameters)
+    - [Alignment Mode](#alignment-mode)
+    - [Structure search from FASTA input](#structure-search-from-fasta-input)
+  - [Databases](#databases)
+    - [Create Custom Databases and Indexes](#create-custom-databases-and-indexes)
+  - [Cluster](#cluster)
+    - [Output](#output-cluster)
+    - [Important Parameters](#important-cluster-parameters)
+  - [Multimer](#multimersearch)
+    - [Output](#multimer-search-output)
+  - [MultimerCluster](#multimercluster)
+- [Main Modules](#main-modules)
+- [Examples](#examples)
 
 ## Webserver 
 Search your protein structures against the [AlphaFoldDB](https://alphafold.ebi.ac.uk/) and [PDB](https://www.rcsb.org/) in seconds using the Foldseek webserver ([code](https://github.com/soedinglab/mmseqs2-app)): [search.foldseek.com](https://search.foldseek.com) 🚀