nicer formatting for mafft functions in documentary

docs/mafft.md

@@ -9,29 +9,13 @@ Tested with MAFFT v7.215 (2014/12/17)
 ## Dependencies
 
   * MAFFT has to be installed
-  * FastaIO
-
-## Usage
-
-```julia
-mafft("examples/fasta/il4.fasta")
-```
-
-Runs mafft with the provided fasta file and returns the alignment in FastaIO dataformat. By default mafft is called with the `--auto` option.
-
-
-```julia
-mafft("examples/fasta/il4.fasta", ["--localpair", "--maxiterate", "1000"])
-```
-
-Calling mafft with custom arguments. Arguments have to be a array of strings. This call is also equivalent to calling:
-
-```julia
- mafft("examples/fasta/il4.fasta", :linsi)
-```
+  * Julia Packages
+    * FastaIO
 
 ## Exported functions
 
+### mafft
+
 ```julia
 mafft(fasta_in::String, preconfiguration=:default)
 ```
@@ -42,6 +26,8 @@ Runs mafft with the provided fasta file and returns the alignment in FastaIO dat
 
 *preconfiguration*: optional commandline arguments for MAFFT (array of strings)
 
+### mafft_from_string
+
 ```julia
 mafft_from_string(fasta_in::String, preconfiguration=:default)
 ```
@@ -52,6 +38,8 @@ Calls MAFFT with the given FASTA string as input and returns aligned FASTA in th
 
 **preconfiguration**: optional commandline arguments for MAFFT (array of strings) 
 
+### mafft_from_fasta
+
 ```julia
 mafft_from_fasta(fasta_in, preconfiguration=:default)
 ```
@@ -62,20 +50,26 @@ Calls MAFFT with the given FASTA in FastaIO format
 
 *preconfiguration*: optional commandline arguments for MAFFT (array of strings)
 
+### mafft_profile
+
 ```julia
 mafft_profile(group1::String, group2::String)
 ```
 Group-to-group alignments
 
 **group1** and **group2** have to be files with alignments. Returns aligned FASTA in the FastaIO dataformat.
 
+### mafft_profile_from_string
+
 ```julia
 mafft_profile_from_string(group1::String, group2::String)
 ```
 Group-to-group alignments with input strings in FASTA format.
 
  **group1** and **group2** have to be strings with alignments in FASTA format.
 
+ ### mafft_profile_from_fasta
+
 ```julia
 mafft_profile_from_fasta(group1, group2)
 ```
@@ -87,28 +81,33 @@ Group-to-group alignments with input in FastaIO format
 ### Helper functions for aligned FASTA
 This module also includes a few helper functions for the FastaIO dataformat (which is returned by the mafft functions of this module).
 
+#### alignment_length
+
 ```julia
 alignment_length(fasta)
 ```
 Returns the length of the alignment.
 
 **fasta**: A FastaIO dataformat object
 
+#### to_aminoacids
+
 ```julia
 to_aminoacids(fasta)
 ```
 Converts a FastaIO-formatted array into an array of BioSeq AminoAcid.
 
 **fasta**: A FastaIO dataformat object
 
+#### print_fasta
+
 ```julia
 print_fasta(fasta)
 ```
 Prints a FastaIO object in a nicely formatted way to the screen.
 
 **fasta**: A FastaIO dataformat object
 
-
 ## Supported pre-configurations (strategies)
 
 The following mafft strategies are supported by built-in preconfigurations which can be used by supplying the function calls with the corresponding symbol (in the parentheses). 
@@ -121,6 +120,25 @@ The following mafft strategies are supported by built-in preconfigurations which
   * NW-NS-i (``:nwnsi``)
   * NW-NS-2 (``:nwns``)
 
+## Usage
+
+```julia
+mafft("examples/fasta/il4.fasta")
+```
+
+Runs mafft with the provided fasta file and returns the alignment in FastaIO dataformat. By default mafft is called with the `--auto` option.
+
+
+```julia
+mafft("examples/fasta/il4.fasta", ["--localpair", "--maxiterate", "1000"])
+```
+
+Calling mafft with custom arguments. Arguments have to be a array of strings. This call is also equivalent to calling:
+
+```julia
+ mafft("examples/fasta/il4.fasta", :linsi)
+```
+
 ## References
 <ul>
 <li>