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diff --git a/docs/tools/agat_convert_bed2gff.md b/docs/tools/agat_convert_bed2gff.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_bed2gff.pl
+# agat\_convert\_bed2gff.pl
 
 ## DESCRIPTION
 
@@ -55,4 +53,3 @@ agat_convert_bed2gff.pl -h
 - **-h** or **--help**
 
     Display this helpful text.
-
diff --git a/docs/tools/agat_convert_embl2gff.md b/docs/tools/agat_convert_embl2gff.md
@@ -1,6 +1,4 @@
-## NAME
-
-gaas\_converter\_embl2gff.pl
+# gaas\_converter\_embl2gff.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_genscan2gff.md b/docs/tools/agat_convert_genscan2gff.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_genscan2gff.pl
+# agat\_convert\_genscan2gff.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_mfannot2gff.md b/docs/tools/agat_convert_mfannot2gff.md
@@ -1,6 +1,4 @@
-## NAME
-
-gaas\_convert\_mfannot2gff.pl
+# gaas\_convert\_mfannot2gff.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_minimap2_bam2gff.md b/docs/tools/agat_convert_minimap2_bam2gff.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_sp\_minimap2\_bam2gff.pl
+# agat\_convert\_sp\_minimap2\_bam2gff.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_sp_gff2bed.md b/docs/tools/agat_convert_sp_gff2bed.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_sp\_gff2bed.pl
+# agat\_convert\_sp\_gff2bed.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_sp_gff2gtf.md b/docs/tools/agat_convert_sp_gff2gtf.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_sp\_gff2gtf.pl
+# agat\_convert\_sp\_gff2gtf.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_sp_gff2tsv.md b/docs/tools/agat_convert_sp_gff2tsv.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_sp\_gff2tsv.pl
+# agat\_convert\_sp\_gff2tsv.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_sp_gff2zff.md b/docs/tools/agat_convert_sp_gff2zff.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_sp\_gff2zff.pl
+# agat\_convert\_sp\_gff2zff.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_convert_sp_gxf2gxf.md b/docs/tools/agat_convert_sp_gxf2gxf.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_convert\_sp\_gxf2gxf.pl
+# agat\_convert\_sp\_gxf2gxf.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_Prokka_inferNameFromAttributes.md b/docs/tools/agat_sp_Prokka_inferNameFromAttributes.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_Prokka\_inferNameFromAttributes.pl
+# agat\_sp\_Prokka\_inferNameFromAttributes.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_add_introns.md b/docs/tools/agat_sp_add_introns.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_add\_introns.pl - This script
+# agat\_sp\_add\_introns.pl - This script
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_add_start_and_stop.md b/docs/tools/agat_sp_add_start_and_stop.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_add\_start\_and\_stop.pl.pl
+# agat\_sp\_add\_start\_and\_stop.pl.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_alignment_output_style.md b/docs/tools/agat_sp_alignment_output_style.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_alignment\_output\_style.pl
+# agat\_sp\_alignment\_output\_style.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_clipN_seqExtremities_and_fixCoordinates.md b/docs/tools/agat_sp_clipN_seqExtremities_and_fixCoordinates.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_clipN\_seqExtremities\_and\_fixCoordinates.pl
+# agat\_sp\_clipN\_seqExtremities\_and\_fixCoordinates.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_compare_two_BUSCOs.md b/docs/tools/agat_sp_compare_two_BUSCOs.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_compare\_two\_BUSCOs.pl
+# agat\_sp\_compare\_two\_BUSCOs.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_compare_two_annotations.md b/docs/tools/agat_sp_compare_two_annotations.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_compare\_two\_annotations.pl
+# agat\_sp\_compare\_two\_annotations.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_complement_annotations.md b/docs/tools/agat_sp_complement_annotations.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_complement\_annotations.pl
+# agat\_sp\_complement\_annotations.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_ensembl_output_style.md b/docs/tools/agat_sp_ensembl_output_style.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_ensembl\_output\_style.pl
+# agat\_sp\_ensembl\_output\_style.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_extract_attributes.md b/docs/tools/agat_sp_extract_attributes.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_extract\_attributes.pl
+# agat\_sp\_extract\_attributes.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_extract_sequences.md b/docs/tools/agat_sp_extract_sequences.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_extract\_sequences.pl
+# agat\_sp\_extract\_sequences.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_by_ORF_size.md b/docs/tools/agat_sp_filter_by_ORF_size.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_by\_ORF\_size.pl
+# agat\_sp\_filter\_by\_ORF\_size.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_by_locus_distance.md b/docs/tools/agat_sp_filter_by_locus_distance.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_by\_locus\_distance.pl
+# agat\_sp\_filter\_by\_locus\_distance.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_by_mrnaBlastValue.md b/docs/tools/agat_sp_filter_by_mrnaBlastValue.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_by\_mrnaBlastValue.pl
+# agat\_sp\_filter\_by\_mrnaBlastValue.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_feature_by_attribute_presence.md b/docs/tools/agat_sp_filter_feature_by_attribute_presence.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_select\_feature\_by\_attribute\_presence.pl
+# agat\_sp\_select\_feature\_by\_attribute\_presence.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_feature_by_attribute_value.md b/docs/tools/agat_sp_filter_feature_by_attribute_value.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_select\_feature\_by\_attribute\_value.pl
+# agat\_sp\_select\_feature\_by\_attribute\_value.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_feature_from_keep_list.md b/docs/tools/agat_sp_filter_feature_from_keep_list.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_feature\_from\_keep\_list.pl
+# agat\_sp\_filter\_feature\_from\_keep\_list.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_feature_from_kill_list.md b/docs/tools/agat_sp_filter_feature_from_kill_list.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_feature\_from\_kill\_list.pl
+# agat\_sp\_filter\_feature\_from\_kill\_list.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_gene_by_intron_numbers.md b/docs/tools/agat_sp_filter_gene_by_intron_numbers.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_gene\_by\_intron\_numbers.pl
+# agat\_sp\_filter\_gene\_by\_intron\_numbers.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_gene_by_length.md b/docs/tools/agat_sp_filter_gene_by_length.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_gene\_by\_length.pl
+# agat\_sp\_filter\_gene\_by\_length.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_incomplete_gene_coding_models.md b/docs/tools/agat_sp_filter_incomplete_gene_coding_models.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_incomplete\_gene\_coding\_models.pl
+# agat\_sp\_filter\_incomplete\_gene\_coding\_models.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_filter_record_by_coordinates.md b/docs/tools/agat_sp_filter_record_by_coordinates.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_filter\_record\_by\_coordinates.pl
+# agat\_sp\_filter\_record\_by\_coordinates.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_fix_cds_phases.md b/docs/tools/agat_sp_fix_cds_phases.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_fix\_cds\_frame.pl
+# agat\_sp\_fix\_cds\_frame.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_fix_features_locations_duplicated.md b/docs/tools/agat_sp_fix_features_locations_duplicated.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_fix\_features\_locations\_duplicated.pl
+# agat\_sp\_fix\_features\_locations\_duplicated.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_fix_fusion.md b/docs/tools/agat_sp_fix_fusion.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_fix\_fusion.pl
+# agat\_sp\_fix\_fusion.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_fix_longest_ORF.md b/docs/tools/agat_sp_fix_longest_ORF.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_fix\_longest\_ORF.pl
+# agat\_sp\_fix\_longest\_ORF.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_fix_overlaping_genes.md b/docs/tools/agat_sp_fix_overlaping_genes.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_fix\_overlaping\_genes.pl
+# agat\_sp\_fix\_overlaping\_genes.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_fix_small_exon_from_extremities.md b/docs/tools/agat_sp_fix_small_exon_from_extremities.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_fix\_small\_exon\_from\_extremities.pl
+# agat\_fix\_small\_exon\_from\_extremities.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_flag_premature_stop_codons.md b/docs/tools/agat_sp_flag_premature_stop_codons.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_flag\_premature\_stop\_codons.pl
+# agat\_sp\_flag\_premature\_stop\_codons.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_flag_short_introns.md b/docs/tools/agat_sp_flag_short_introns.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_flag\_short\_introns.pl
+# agat\_sp\_flag\_short\_introns.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_functional_statistics.md b/docs/tools/agat_sp_functional_statistics.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_functional\_statistics.pl
+# agat\_sp\_functional\_statistics.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_gxf_to_gff3.md b/docs/tools/agat_sp_gxf_to_gff3.md
@@ -1,6 +1,4 @@
-## /!\ replaced by [agat_convert_sp_gxf2gxf](https://github.com/NBISweden/AGAT/wiki/agat_convert_sp_gxf2gxf) since AGAT v0.3.0
-
-## NAME
+# ## NAME
 
 agat\_sp\_gxf\_to\_gff3.pl
 

diff --git a/docs/tools/agat_sp_keep_longest_isoform.md b/docs/tools/agat_sp_keep_longest_isoform.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_keep\_longest\_isoform.pl
+# agat\_sp\_keep\_longest\_isoform.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_kraken_assess_liftover.md b/docs/tools/agat_sp_kraken_assess_liftover.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_kraken\_assess\_lift\_coverage.pl
+# agat\_sp\_kraken\_assess\_lift\_coverage.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_list_short_introns.md b/docs/tools/agat_sp_list_short_introns.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_list\_short\_introns.pl
+# agat\_sp\_list\_short\_introns.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_load_function_from_protein_align.md b/docs/tools/agat_sp_load_function_from_protein_align.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_load\_function\_from\_protein\_align.pl
+# agat\_sp\_load\_function\_from\_protein\_align.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_manage_IDs.md b/docs/tools/agat_sp_manage_IDs.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_manage\_IDs.pl
+# agat\_sp\_manage\_IDs.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_manage_UTRs.md b/docs/tools/agat_sp_manage_UTRs.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_manage\_UTRs.pl
+# agat\_sp\_manage\_UTRs.pl
 
 ## DESCRIPTION
 

diff --git a/docs/tools/agat_sp_manage_attributes.md b/docs/tools/agat_sp_manage_attributes.md
@@ -1,6 +1,4 @@
-## NAME
-
-agat\_sp\_manage\_attributes.pl
+# agat\_sp\_manage\_attributes.pl
 
 ## DESCRIPTION