homology

McTavishLab · Aug 10, 2021 · bebe7c8 · bebe7c8
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diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,7 @@ IS_README <- TRUE
 
 <img align="left" width="250" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
 
-# Physcraper
+# Welcome to Physcraper’s repository!
 
 [![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)
 
@@ -26,9 +26,6 @@ IS_README <- TRUE
 <p></p>
 
 
-## Automated gene tree updating with the Open Tree of Life!
-
-
 ```{r child="docs/mds/intro.md"}
 
 ```

diff --git a/docs/mds/description.md b/docs/mds/description.md
@@ -4,19 +4,19 @@ 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
 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 homologous to genetic sequences used to construct existing
+have the advantage of being orthologous to genetic sequences used to construct existing
 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) to sequences in the initial DNA alignment.
+homologous (both orthologs and paralogs, see [FAQs](https://physcraper.readthedocs.io/en/stable/faq.html)) 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
 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
 monophyletic group, or within the taxonomic scope of the ingroup of the starting tree.
 
-These automated trees can provide a quick inference of potential phylogenetic relationships,
+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.
 
 <br/>
@@ -32,7 +32,7 @@ The Physcraper framework consists of 4 general steps. The methodology is further
 
 ## The Open Tree of Life
 
-The Open Tree of Life (OpenTree) is a project that unites expert, peer-reviwed [phylogenetic inferences](https://github.com/OpenTreeOfLife/phylesystem-1) and
+The Open Tree of Life (OpenTree) is a project that unites expert, peer-reviewed [phylogenetic inferences](https://github.com/OpenTreeOfLife/phylesystem-1) and
 [taxonomy](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.3)
 to generate a [synthetic tree](https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott93302) estimate of species relationships across all life.
 

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="left" width="180" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
+<img align="right" width="180" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
diff --git a/docs/mds/intro-requirements.md b/docs/mds/intro-requirements.md
@@ -3,15 +3,16 @@
 Physcraper requires the user to install:
 
 - [Anaconda](https://docs.anaconda.com/anaconda/install/) <br>
-*Anaconda Software Distribution. Computer software. Vers. 4.8.0. Anaconda, July. 2021. Web. <https://anaconda.com>*,
-- [Virtualenv](https://pypi.org/project/virtualenv/),
+*Anaconda Software Distribution. Computer software. Vers. 4.8.0. Anaconda, July. 2021. Web. <https://anaconda.com>*
+- [Virtualenv](https://pypi.org/project/virtualenv/)
 - [MUSCLE](https://www.ebi.ac.uk/Tools/msa/muscle/) <br>
 *Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7.* doi: [10.1093/nar/gkh340](https://doi.org/10.1093/nar/gkh340)
 - [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) <br>
 *Stamatakis, Alexandros. "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies." Bioinformatics 30.9 (2014): 1312-1313.* doi: [10.1093/bioinformatics/btu033](https://doi.org/10.1093/bioinformatics/btu033)
-- [BLAST +](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) if using a local genetic database.
-Note that BLAST + is automatically installed with a [Physcraper installation using Anaconda](https://physcraper.readthedocs.io/en/stable/install.html#anaconda-virtual-environment). <br>
-*Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).* doi: [10.1186/1471-2105-10-421](https://doi.org/10.1186/1471-2105-10-421).
+- [BLAST +](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) <br>
+This software is only needed if using a local genetic database.
+Note that BLAST + is automatically installed when [installing Physcraper using Anaconda](https://physcraper.readthedocs.io/en/stable/install.html#anaconda-virtual-environment). <br>
+*Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).* doi: [10.1186/1471-2105-10-421](https://doi.org/10.1186/1471-2105-10-421)
 
 
 Physcraper relies on the following Python packages that are automatically installed:

diff --git a/docs/mds/intro.md b/docs/mds/intro.md
@@ -1,3 +1,5 @@
+## Automated gene tree updating <br> with the Open Tree of Life\!
+
 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 in a 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: