updated README.md

Author: Tobias Hofmann

docs/index.md

@@ -39,12 +39,3 @@ Some functions in this pipeline are inspired by scripts from the [Phyluce pipeli
 **Andermann T.**, Cano Á., Zizka A., Bacon C., Antonelli A. 2018. SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments. PeerJ 6:e5175 [https://doi.org/10.7717/peerj.5175](https://doi.org/10.7717/peerj.5175)
 
 Faircloth B.C., PHYLUCE is a software package for the analysis of conserved genomic loci, Bioinformatics, Volume 32, Issue 5, 1 March 2016, Pages 786–788, [https://doi.org/10.1093/bioinformatics/btv646](https://doi.org/10.1093/bioinformatics/btv646)
-
-Guide
-=====
-
-.. toctree::
-   :maxdepth: 2
-
-   markdown/main_doc
-