README.md v2024-04-21; updated info on release 2.2.1 and associated D…

…ocker image 20240418; fixed typos

README.md

@@ -5,7 +5,7 @@
 [![GPLv3-like license](https://img.shields.io/badge/License-GPLv3-blue.svg)](./LICENSE.txt)
 [![DockerHub](https://badgen.net/badge/icon/docker?icon=docker&label)](https://hub.docker.com/r/vinuesa/get_phylomarkers)
 
-**GET_PHYLOMARKERS** ([Vinuesa et al., 2018](https://www.frontiersin.org/articles/10.3389/fmicb.2018.00771/full)) **is an open-source software package for selecting optimal markers for microbial phylogenomics and species tree estimation**. It implements a [** bioinformatics pipeline**](https://www.frontiersin.org/files/Articles/351767/fmicb-09-00771-HTML/image_m/fmicb-09-00771-g001.jpg) to filter core-genome gene clusters computed by the companion package [**GET_HOMOLOGUES**](https://github.com/eead-csic-compbio/get_homologues), and selects only those with optimal attributes for phylogenetic inference using maximum likelihood (ML). The multiple sequence alignments of the filtered loci are concatenated into a supermatrix to estimate a species tree using the state-of-the-art fast ML tree searching algorithms [FastTree](http://www.microbesonline.org/fasttree) or [IQ-TREE](http://www.iqtree.org). It also estimates ML and parsimony trees from the pan-genome matrix, including unsupervised learning methods.  We have also tested it successfully with **plant coding sequences** (details [here](https://github.com/vinuesa/get_phylomarkers?tab=readme-ov-file#manual-and-tutorials)).
+**GET_PHYLOMARKERS** ([Vinuesa et al., 2018](https://www.frontiersin.org/articles/10.3389/fmicb.2018.00771/full)) **is an open-source software package for selecting optimal markers for microbial phylogenomics and species tree estimation**. It implements a [**bioinformatics pipeline**](https://www.frontiersin.org/files/Articles/351767/fmicb-09-00771-HTML/image_m/fmicb-09-00771-g001.jpg) to filter core-genome gene clusters computed by the companion package [**GET_HOMOLOGUES**](https://github.com/eead-csic-compbio/get_homologues), and selects only those with optimal attributes for phylogenetic inference using maximum likelihood (ML). The multiple sequence alignments of the filtered loci are concatenated into a supermatrix to estimate a species tree using the state-of-the-art fast ML tree searching algorithms [FastTree](http://www.microbesonline.org/fasttree) or [IQ-TREE](http://www.iqtree.org). It also estimates ML and parsimony trees from the pan-genome matrix, including unsupervised learning methods.  We have also tested it successfully with **plant coding sequences** (details [here](https://github.com/vinuesa/get_phylomarkers?tab=readme-ov-file#manual-and-tutorials)).
 
 ## GET_PHYLOMARKERS 2
 
@@ -24,7 +24,7 @@ Starting with **release 2.0.0** (2022-11-20), [GET_PHYLOMARKERS](https://github.
 - Complex protein mixture models are used for concatenated protein alignments
 
 
-[**Release 2.2.1 (2024-04-16)**](https://github.com/vinuesa/get_phylomarkers/releases/tag/v2.2.1) includes a static binary of [**snp-sites**]((https://github.com/sanger-pathogens/snp-sites), which is called by <code>run_get_phylomarkers_pipeline.sh</code> >= v2.8.1.0_2024-04-15 under run mode 2 (-R 2, population genetics) to generate **SNP matrices in FASTA and [VCF](https://samtools.github.io/hts-specs/VCFv4.2.pdf) formats** from the concatenated alignments of filtered, highly informative, and neutral loci. The FASTA SNP matrix is used for estimating a **ML population tree**. Thanks to Alfredo Hernández @ccg_unam for compiling snp-sites-static.
+[**Release 2.2.1 (2024-04-16)**](https://github.com/vinuesa/get_phylomarkers/releases/tag/v2.2.1) includes a static binary of [**snp-sites**](https://github.com/sanger-pathogens/snp-sites), which is called by <code>run_get_phylomarkers_pipeline.sh</code> >= v2.8.1.0_2024-04-15 under run mode 2 (-R 2, population genetics) to generate **SNP matrices in FASTA and [VCF](https://samtools.github.io/hts-specs/VCFv4.2.pdf) formats** from the concatenated alignments of filtered, highly informative, and neutral loci. The FASTA SNP matrix is used for estimating a **ML population tree**. Thanks to Alfredo Hernández @ccg_unam for compiling snp-sites-static.
 
 - This release was used to build the latest [**Docker GET_PHYLOMARKERS image (20240418)**](https://hub.docker.com/r/vinuesa/get_phylomarkers) ready to pull from Docker Hub (<code>docker pull vinuesa/get_phylomarkers:latest</code>. This is a significantly lighter (2G.0B) image than the previous one (v20240414 (2.09GB), because several unnecessary R packages were removed. On [Dockerhub](https://hub.docker.com/r/vinuesa/get_phylomarkers), 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](https://github.com/vinuesa/get_phylomarkers) pipeline.