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NBISweden · Apr 14, 2021 · 8869f6f · 8869f6f
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diff --git a/docs/index.rst b/docs/index.rst
@@ -13,7 +13,7 @@ Contents
 ========
 
 .. toctree::
-   :maxdepth: 1
+   :maxdepth: 2
    :caption: General:
 
    the_format.md
@@ -22,8 +22,10 @@ Contents
    topological-sorting-of-gff-features.md
    troubleshooting.md
 
+.. toctree::
    :maxdepth: 0
    :caption: List of tools:
+
    tools/agat_convert_bed2gff.md
    tools/agat_convert_embl2gff.md
    tools/agat_convert_genscan2gff.md

diff --git a/docs/topological-sorting-of-gff-features.md b/docs/topological-sorting-of-gff-features.md
@@ -8,7 +8,7 @@ It might be critical to have a GFF/GTF file properly sorted:
 
 Zhigang Lu has made a nice post about his experience trying to find a way to get a correct topological sorting. See [here](https://zhiganglu.com/post/sort-gff-topologically/).
 
-## Table of Contents
+### Table of Contents
 
  * [Tests summary](#test-summary)
  * [Example 1](#example-1)
@@ -27,7 +27,7 @@ Zhigang Lu has made a nice post about his experience trying to find a way to get
      * [gffread](#gffread-2)
 
 
-### Tests summary
+#### Tests summary
 
 tool | option in command line | Type of sorting | Comment
 -- | -- | -- | -- |
@@ -37,11 +37,11 @@ tool | option in command line | Type of sorting | Comment
 [GFF3sort](https://github.com/billzt/gff3sort) | --precise | by chromosomes and positions then attribute with Parent attribute first.  | move lines with "Parent=" attributes (case insensitive) behind lines without "Parent=" attributes. The goal of GFF3sort is not to obtain a topological sorting but rather getting something that could be indexed optimally by third part tools.
 [gffread](https://github.com/gpertea/gffread) | | By default, chromosomes are kept in the order they were found. With --sort-alpha parameter the chromosomes (reference sequences) are sorted alphabetically | /!\ Some feature types are lost e.g. `gene`, `three_prime_UTR`, `five_prime_UTR`, etc...
 
-## Example 1
+### Example 1
 
 This test is based on the file used by [Zhigang Lu](https://zhiganglu.com/post/sort-gff-topologically/)
 
-### The GFF file to sort
+#### The GFF file to sort
 
 ```
 ##gff-version 3
@@ -76,9 +76,9 @@ SM_V7_1	AUGUSTUS	five_prime_UTR	151133	151162	.	-	.	Parent=Smp_315690.1
 SM_V7_1	AUGUSTUS	five_prime_UTR	151133	151162	.	-	.	Parent=Smp_315690.2
 ```
 
-### Results
+#### Results
 
-#### AGAT
+##### AGAT
 
 AGAT v0.4.0  
 
@@ -117,7 +117,7 @@ SM_V7_1	AUGUSTUS	five_prime_UTR	151133	151162	.	-	.	ID=five_prime_utr-2;Parent=S
 SM_V7_1	AUGUSTUS	three_prime_UTR	103403	103440	.	-	.	ID=three_prime_utr-2;Parent=Smp_315690.2
 ```
 
-#### GenomeTools
+##### GenomeTools
 
 GenomeTools 1.6.1
 
@@ -194,7 +194,7 @@ SM_V7_1	AUGUSTUS	five_prime_UTR	151133	151162	.	-	.	Parent=Smp_315690.2
 ###
 ```
 
-#### GFF3sort
+##### GFF3sort
 
 GFF3sort 0.1.a1a2bc9
 
@@ -233,7 +233,7 @@ SM_V7_1	AUGUSTUS	five_prime_UTR	151133	151162	.	-	.	Parent=Smp_315690.1
 SM_V7_1	AUGUSTUS	five_prime_UTR	151133	151162	.	-	.	Parent=Smp_315690.2
 ```
 
-#### gffread
+##### gffread
 
 gffread v0.11.4
 
@@ -269,11 +269,11 @@ SM_V7_1	AUGUSTUS	CDS	145395	145678	.	-	2	Parent=Smp_315690.2
 SM_V7_1	AUGUSTUS	CDS	151075	151132	.	-	0	Parent=Smp_315690.2
 ```
 
-## Example 2
+### Example 2
 
 This test is based on the file used by [GFF3sort](https://github.com/billzt/gff3sort)
 
-### The GFF file to sort
+#### The GFF file to sort
 
 ```
 ##gff-version 3
@@ -293,9 +293,9 @@ A01	Cufflinks	exon	3637	3726	.	-	.	Parent=XLOC_001154.42
 A01	Cufflinks	exon	5329	6386	.	-	.	Parent=XLOC_001154.42
 ```
 
-### Results
+#### Results
 
-#### AGAT
+##### AGAT
 
 AGAT v0.4.0  
 
@@ -319,7 +319,7 @@ A01	Cufflinks	exon	3637	3726	.	-	.	ID=exon-9;Parent=XLOC_001154.42
 A01	Cufflinks	exon	5329	6386	.	-	.	ID=exon-10;Parent=XLOC_001154.42
 ```
 
-#### GenomeTools
+##### GenomeTools
 
 GenomeTools 1.6.1
 
@@ -380,7 +380,7 @@ SM_V7_1	AUGUSTUS	five_prime_UTR	151133	151162	.	-	.	Parent=Smp_315690.2
 ###
 ```
 
-#### GFF3sort
+##### GFF3sort
 
 GFF3sort 0.1.a1a2bc9
 
@@ -402,7 +402,7 @@ A01	Cufflinks	exon	5329	5408	.	-	.	Parent=XLOC_001154.41
 A01	Cufflinks	exon	5994	6154	.	-	.	Parent=XLOC_001154.41
 ```
 
-#### gffread 
+##### gffread 
 
 gffread v0.11.4