improved repository README.md with TOC and links to sections

README.md

@@ -77,17 +77,17 @@ with contributions from Carlos P Cantalapiedra, Alvaro Rodriguez del Rio, Ruben
 Sancho, Roland Wilhelm, David A Wilkinson and many others (see [CHANGES.txt](./CHANGES.txt)). 
 It also includes code and binaries from other authors:
 
- OrthoMCL v1.4 (www.orthomcl.org , PubMed:12952885)
- mcl v14-137 (http://micans.org/mcl , PubMed=11917018)
- COGtriangles v2.1 (sourceforge.net/projects/cogtriangles , PubMed=20439257)
- NCBI Blast-2.16.1+ (blast.ncbi.nlm.nih.gov , PubMed=9254694,20003500)
- BioPerl v1.5.2 (www.bioperl.org , PubMed=12368254)
- HMMER 3.1b2 (http://hmmer.org)
- Pfam (http://pfam.xfam.org , PubMed=19920124)
- PHYLIP 3.695 (http://evolution.genetics.washington.edu/phylip) 
- Transdecoder r20140704 (http://transdecoder.github.io , PubMed=23845962)
- MVIEW 1.60.1 (https://github.com/desmid/mview, PubMed=9632837)
- diamond 0.8.25 (https://github.com/bbuchfink/diamond, PubMed=25402007)
+    OrthoMCL v1.4 (www.orthomcl.org , PubMed:12952885)
+    mcl v14-137 (http://micans.org/mcl , PubMed=11917018)
+    COGtriangles v2.1 (sourceforge.net/projects/cogtriangles , PubMed=20439257)
+    NCBI Blast-2.16.1+ (blast.ncbi.nlm.nih.gov , PubMed=9254694,20003500)
+    BioPerl v1.5.2 (www.bioperl.org , PubMed=12368254)
+    HMMER 3.1b2 (http://hmmer.org)
+    Pfam (http://pfam.xfam.org , PubMed=19920124)
+    PHYLIP 3.695 (http://evolution.genetics.washington.edu/phylip) 
+    Transdecoder r20140704 (http://transdecoder.github.io , PubMed=23845962)
+    MVIEW 1.60.1 (https://github.com/desmid/mview, PubMed=9632837)
+    diamond 0.8.25 (https://github.com/bbuchfink/diamond, PubMed=25402007)
 
 ## Graphical summary