more readme updates

McTavishLab · Aug 10, 2021 · 7ef857a · 7ef857a
1 parent 5cd9129
commit 7ef857a
Show file tree

Hide file tree

Showing 4 changed files with 18 additions and 10 deletions.
diff --git a/README.md b/README.md
@@ -31,6 +31,13 @@ from the [Open Tree of
 Life](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302)
 project.
 
+Physcraper also leverages on programmatic tools from the
+[TreeBASE](https://treebase.org/treebase-web/urlAPI.html) project and
+[NCBI](https://www.ncbi.nlm.nih.gov/home/develop/api/), as well as
+multiple software projects listed as [requirements](#Requirements)
+below, to create an automatic and reproducible workflow for
+phylogenetics.
+
 You are now on the code repository. Please refer to Physcraper’s
 [documentation website](https://physcraper.readthedocs.io/en/latest/)
 for more details

diff --git a/docs/mds/description.md b/docs/mds/description.md
@@ -1,23 +1,22 @@
 ## The Physcraper framework
 
 While genome scale data is increasing rapidly, there are still large quantities
-of gene-sequence data being uploaded to the US National Center on Biotechnology
+of single locus nucleotide sequence data being uploaded to the US National Center on Biotechnology
 Information (NCBI) database [GenBank](https://www.ncbi.nlm.nih.gov/genbank/statistics/).
 These data are often appropriate for looking at phylogenetic relationships, and
-have the advantage of being orthologous to genetic sequences used to construct existing
-trees.
+have the advantage of being orthologous to genetic sequences that have been used to construct existing phylogenetic trees.
 
-If you have access to a single gene or multilocus DNA alignment, and a phylogenetic tree, Physcraper automates
-adding DNA sequences of new lineage samples into your tree by using [Open Tree of Life](#the-open-tree-of-life) tools to reconcile taxonomies, and the [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi) algorithm to search for loci in the [GenBank](https://www.ncbi.nlm.nih.gov/genbank/statistics/) genetic database that are likely to be
-homologous (both orthologs and paralogs, see [FAQs](https://physcraper.readthedocs.io/en/stable/faq.html)) to sequences in the initial DNA alignment.
+If you have access to a single gene or multilocus nucleotide alignment, and a phylogenetic tree, Physcraper automates
+adding nucleotide sequences of new lineage samples into your tree by using [Open Tree of Life](#the-open-tree-of-life) tools to reconcile Taxonomy, and the [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi) algorithm to search for loci in the [GenBank](https://www.ncbi.nlm.nih.gov/genbank/statistics/) genetic database that are likely to be
+locally similar to sequences in the initial DNA alignment.
 
-By using a starting alignment and tree, Physcraper takes advantage of DNA loci and homology hypotheses (ideally orthology) that
+By using a starting alignment and tree, Physcraper takes advantage of DNA loci alignments as  homology hypotheses (ideally orthology, see [FAQs](https://physcraper.readthedocs.io/en/stable/faq.html)) that
 previous researchers have assessed, curated, and deemed appropriate for the phylogenetic scope.
-The sequences added during the BLAST search are limited either to a user specified taxon or
+The sequences added during a BLAST search are limited either to a user specified taxon or
 monophyletic group, or within the taxonomic scope of the ingroup of the starting tree.
 
 These automated, reproducible trees can provide a quick inference of potential phylogenetic relationships,
-of problems in the taxonomic assignments of sequences, paralogy and orthology, as well as flag areas of potential systematic interest.
+as well as flag problems in the taxonomic assignments of sequences, paralogy and orthology, and areas of potential systematic interest.
 
 <br/>
 

diff --git a/docs/mds/intro-header.md b/docs/mds/intro-header.md
@@ -1,4 +1,4 @@
 
 [![Build Status](https://travis-ci.org/McTavishLab/physcraper.svg?branch=main)](https://travis-ci.org/McTavishLab/physcraper)[![Documentation](https://readthedocs.org/projects/physcraper/badge/?version=latest&style=flat)](https://physcraper.readthedocs.io/en/latest/)[![codecov](https://codecov.io/gh/McTavishLab/physcraper/branch/main/graph/badge.svg)](https://codecov.io/gh/McTavishLab/physcraper)
 
-<img align="right" width="200" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
+<img align="right" width="250" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
diff --git a/docs/mds/intro.md b/docs/mds/intro.md
@@ -3,3 +3,5 @@
 Use a phylogenetic tree and a DNA alignment to automatically find and add nucleotide sequences from a genetic database, to reproducibly improve and advance phylogenetic knowledge within a biological group.
 
 Physcraper relies on [taxonomic](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.3) and [phylogenetic](https://github.com/OpenTreeOfLife/phylesystem-1) resources and [programmatic tools](https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs) from the [Open Tree of Life](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302) project.
+
+Physcraper also leverages on programmatic tools from the [TreeBASE](https://treebase.org/treebase-web/urlAPI.html) project and [NCBI](https://www.ncbi.nlm.nih.gov/home/develop/api/), as well as multiple software projects listed as [requirements](#Requirements) below, to create an automatic and reproducible workflow for phylogenetics.