Remove software requirements from index page; changed useful JVM options

docs/source/index.rst

@@ -44,18 +44,9 @@ PanTools currently provides these functionalities:
 -  Gene classification
 -  Phylogenetic methods
 
-Requirements
+Installation
 ------------
 
--  \ **Java Virtual Machine**\  version 1.8 or higher, Add path to the
-   java executable to your OS path environment variable.
--  \ **KMC**\ : A disk-based k-mer counter, After downloading the
-   appropriate version (linux, macos or windows), add path to the *kmc*
-   and *kmc_tools* executables to your OS path environment variable.
--  \ **MCL**\ : The Markov Clustering Algorithm, After downloading and
-   compiling the software, add path to the *mcl* executable to your OS
-   path environment variable.
-
 For installing and configuring all required software, please see our
 :doc:`/getting_started/install` page.
 
@@ -67,15 +58,16 @@ the command line by:
 
 .. substitution-code-block:: bash
 
-   $ java <JVM options> -jar pantools-|ProjectVersion|.jar <subcommand> <arguments>
+   $ pantools <JVM options> <subcommand> <arguments>
 
-| **Useful JVM options**
-| - **-server** : To optimize JIT compilations for higher performance
-| - **-Xmn(a number followed by m/g)** : Minimum heap size in mega/giga
-  bytes
-| - **-Xmx(a number followed by m/g)** : Maximum heap size in mega/giga
-  bytes
+**Useful JVM options:**
 
+-  **-Xmn(a number followed by m/g)** : Minimum heap size in mega/giga
+   bytes
+-  **-Xmx(a number followed by m/g)** : Maximum heap size in mega/giga
+   bytes
+-  **-XX:StartFlightRecording=filename=<name>.jfr,disk=true** : Enable
+   the Flight Recorder
 
 Options
 -------