README.md v2024-04-15.2: fixed typo; better structured info on releas…

…e v2.2.0, and changes made on 2024-04-15

README.md

@@ -13,11 +13,18 @@ Starting with **release 2.0.0** (2022-11-20), a **concatenation-independent spec
  **Release 2.1.0** (2024-03-31) implemented the **maximal matched-pairs tests** to asses violations of the data to the Stationarity, Reversibility, and Homogeneity (SRH) assumptions made by maximum-likelihood phylogenetic models, as implemented in [IQ-TREE](http://www.iqtree.org/). In addition, [**ASTRAL-IV**](https://github.com/chaoszhang/ASTER/blob/master/tutorial/astral4.md) is used to estimate the species tree directly from the filtered ML source gene trees, which computes terminal and internal branch lengths in substitution-per-site units.
 
  [**Release 2.2.0** (v2.2.0, 2024-04-14)](https://github.com/vinuesa/get_phylomarkers/releases/tag/2.2.0) contains new features, significant code improvements, binary updates, and some bug fixes. Among the new features, we would like to highlight the following ones:
+
 -significant extension of run mode 2 (<code>run_get_phylomarkers_pipeline.sh -R 2</code>) for **population genetics** (multiple sequences from the same species):
-- <code>run_get_phylomarkers_pipeline.sh</code> now also calls the C binary [**WEIGHTED-ASTRAL**](https://github.com/chaoszhang/ASTER) to estimate a species tree using as input the filtered gene trees estimated by [iqtree2](http://www.iqtree.org/) or [FastTree](http://www.microbesonline.org/fasttree/) from the core-genome clusters computed by [get_homologues](https://github.com/eead-csic-compbio/get_homologues). 
-- The main script <code>run_get_phylomarkers_pipeline.sh</code> added complex protein mixture models for concatenated protein alignments, prints script invocation arguments to STDOU at the beginning of the run, and prints a summary results of the different filtering steps before exiting. Read the [**Release v2.2.0**)](https://github.com/vinuesa/get_phylomarkers/releases/tag/2.2.0) notes for further details. Note that users of this release interested in run mode 2 (-R 2) for to compute a population tree, will need to install [snp-sites](https://github.com/sanger-pathogens/snp-sites), as explained in the current [INSTALL.md notes](https://github.com/vinuesa/get_phylomarkers/blob/master/INSTALL.md). 
+- <code>run_get_phylomarkers_pipeline.sh</code> now also calls the C binary [**WEIGHTED-ASTRAL**](https://github.com/chaoszhang/ASTER) to estimate a species tree using as input the filtered gene trees estimated by [iqtree2](http://www.iqtree.org/) or [FastTree](http://www.microbesonline.org/fasttree/) from the core-genome clusters computed by [get_homologues](https://github.com/eead-csic-compbio/get_homologues).
+
+- The main script <code>run_get_phylomarkers_pipeline.sh</code> added complex protein mixture models for concatenated protein alignments, prints script invocation arguments to STDOU at the beginning of the run, and prints a summary results of the different filtering steps before exiting. Read the [**Release v2.2.0**)](https://github.com/vinuesa/get_phylomarkers/releases/tag/2.2.0) notes for further details.
+
+- Users of this release interested in run mode 2 (-R 2) to compute a population tree, will need to install [snp-sites](https://github.com/sanger-pathogens/snp-sites), as explained in the current [INSTALL.md notes](https://github.com/vinuesa/get_phylomarkers/blob/master/INSTALL.md).
+
+- Linux users that cloned the the [GET_PHYLOMARKERS GitHub repository](https://github.com/vinuesa/get_phylomarkers) on **2024-04-15**, or later, will not have to install [snp-sites](https://github.com/sanger-pathogens/snp-sites) manually, because a static binary is provided (bin/linux/snp-sites-static), which is called by <code>run_get_phylomarkers_pipeline.sh v2.8.1.0_2024-04-15</code>. Thanks to Alfredo Hernández @ccg_unam for compiling snp-sites-static.
+
+- [**Release 2.2.0** (2024-04-14)](https://github.com/vinuesa/get_phylomarkers/releases/tag/2.2.0) was used to build the *latest* **Docker image** ready to pull from [**Docker Hub**](https://hub.docker.com/r/vinuesa/get_phylomarkers). On Dockerhub, you will find detailed instructions on installing and configuring the Docker client on your machine, pulling the latest image, and running the containerized instance of the GET_PHYLOMARKERS pipeline.
 
-[**Release 2.2.0** (2024-04-14)](https://github.com/vinuesa/get_phylomarkers/releases/tag/2.2.0) was used to build the *latest* **Docker image** ready to pull from [**Docker Hub**](https://hub.docker.com/r/vinuesa/get_phylomarkers). On Dockerhub, you will find detailed instructions on installing and configuring the Docker client on your machine, pulling the latest image, and running the containerized instance of the GET_PHYLOMARKERS pipeline.  
 
  **GET_PHYLOMARKERS** can also estimate **ML and parsimony trees from the pan-genome matrix**, including unsupervised learning methods to determine the optimal number of clusters from the pan-genome and average genomic distance matrices. A detailed [**manual**](https://vinuesa.github.io/get_phylomarkers/#get_phylomarkers-manual) and step-by-step [**tutorials**](https://vinuesa.github.io/get_phylomarkers/#get_phylomarkers-tutorial) document the software and help the user to get up and running quickly. For convenience, [**html**](https://vinuesa.github.io/get_phylomarkers/) and [**markdown**](https://github.com/vinuesa/get_phylomarkers/blob/master/docs/GET_PHYLOMARKERS_manual.md) versions of the documentation material are available.