minor Markdown cleanup

Author: alexdonath

Orthograph_Quality_Checker/README.md

@@ -1,18 +1,14 @@
 # Orthograph_Quality_Checker.py
 
-**Orthograph_Quality_Checker** performs a quality assessment of transcriptome assemblies based on orthology predictions with [Orthograph](https://github.com/mptrsen/Orthograph)[^1].
+**Orthograph_Quality_Checker** performs a quality assessment of transcriptome assemblies based on orthology predictions with [Orthograph](https://github.com/mptrsen/Orthograph)<sup>[1](#one)</sup>.
 
 ## System requirements
 
----
-
 * Python 3.6.4 or newer
 * Required Python modules: `argparse`, `Bio`, `operator`, `os`, `re`, `shutil`, `sys`
 
 ## Parameters
 
----
-
 The program has three parameters:
 
 `-c/--config` (mandatory)
@@ -29,8 +25,6 @@ Setting `--reuse_tmp` allows you to re-use the summary files from a previous run
 
 ## The config file
 
----
-
 The config file has to be in text format; any file suffix will do.
 
 An example config file could look like this:
@@ -52,15 +46,11 @@ All paths have to be either absolute or relative to the location of `Orthograph_
 
 ## Data preparation
 
----
-
 In order for the program to work properly, the structure of the directory tree in the directory specified using the tag `ORTHOGRAPH=` has to look like this:
 `ORTHOGRAPH/ASSEMBLER/TAXON/aa`
 
 ## The output
 
----
-
 The final output is a tab-separated spreadsheet file (`Summarized_Orthograph_results.tsv`) that can be opened in a text editor or a spreadsheet editor like Excel.
 The first column in the file contains the taxon names. The following fields in the same row each correspond to one assembly of this taxon.
 
@@ -73,4 +63,4 @@ There are four values in each of those fields:
 
 ---
 
-[^1] Petersen, M., Meusemann, K., Donath, A. et al. Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. BMC Bioinformatics 18, 111 (2017). [https://doi.org/10.1186/s12859-017-1529-8](https://doi.org/10.1186/s12859-017-1529-8)
+<a name="one">[1]</a> Petersen, M., Meusemann, K., Donath, A. et al. Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. BMC Bioinformatics 18, 111 (2017). [https://doi.org/10.1186/s12859-017-1529-8](https://doi.org/10.1186/s12859-017-1529-8)

Remove_outliers/README.md

@@ -19,4 +19,4 @@ If not already present, the script will create a directory `aa_outliers_removed/
 
 ---
 
-[^1] [https://github.com/alexdonath/checker_complete-v2](https://github.com/alexdonath/checker_complete-v2)
+<a name="one">[1]</a> [https://github.com/alexdonath/checker_complete-v2](https://github.com/alexdonath/checker_complete-v2)

Remove_reference_sequences/README.md

@@ -9,14 +9,12 @@ The script removes all sequences belonging to reference species from the alignme
 
 ## Other requirements
 
-
 The script has to be in the same directory as the files from which the reference sequences are to be removed.
 
 Note that input files have to have the ending `.fas[ta]`.
 
 ## Output
 
-
 It will automatically create a subdirectory named `no_refseqs/`, in which the modified files will be saved.
 
 ---