Merge pull request #34 from TurakhiaLab/ang037-patch-1

Updated acronym

README.md

@@ -1,6 +1,6 @@
 <div align="center">
 
-# Reference-free Orthology-free Alignment-free DIscordance aware Estimation of Species tree (ROADIES)
+# Reference-free Orthology-free Annotation-free DIscordance aware Estimation of Species tree (ROADIES)
 
 [license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg 
 [license-link]: https://github.com/TurakhiaLab/ROADIES/blob/main/LICENSE
@@ -37,7 +37,7 @@
 
 ## <a name="overview"></a> Introduction
 
-Welcome to the official repository of ROADIES, a novel pipeline designed for phylogenetic tree inference of the species directly from their raw genomic assemblies. ROADIES offers a fully automated, easy-to-use, scalable solution, eliminating any error-prone manual steps and providing unique flexibility in adjusting the tradeoff between accuracy and runtime. 
+Welcome to the official repository of ROADIES, a novel pipeline designed for phylogenetic tree inference of the species directly from their raw genomic assemblies. ROADIES offers a fully automated, easy-to-use, scalable solution, eliminating any manual steps and providing unique flexibility in adjusting the tradeoff between accuracy and runtime. 
 
 **For more detailed information on all the features and settings of ROADIES, please refer to our [Wiki](https://turakhialab.github.io/ROADIES/).**
 

docs/index.md

@@ -4,22 +4,22 @@
 
 </div>
 
-# Reference-free Orthology-free Alignment-free DIscordance aware Estimation of Species tree (ROADIES)
+# Reference-free Orthology-free Annotation-free DIscordance aware Estimation of Species tree (ROADIES)
 
 ## ROADIES Video Tutorial
 
 <iframe width="1000" height="600" src="https://www.youtube.com/embed/1sR741TvZnM?si=xfktnTaQj4LUsNp0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
 
 ## Introduction
 
-Welcome to the official wiki of ROADIES, a novel pipeline designed for phylogenetic tree inference of the species directly from their raw genomic assemblies. ROADIES offers a fully automated, easy-to-use, scalable solution, eliminating any error-prone manual steps and providing unique flexibility in adjusting the tradeoff between accuracy and runtime. 
+Welcome to the official wiki of ROADIES, a novel pipeline designed for phylogenetic tree inference of the species directly from their raw genomic assemblies. ROADIES offers a fully automated, easy-to-use, scalable solution, eliminating any manual steps and providing unique flexibility in adjusting the tradeoff between accuracy and runtime. 
 <br>
 
 ## Key Features
 - **Reference-free**: ROADIES ensures unbiased results by eliminating reference bias, enabling accurate species tree inference by randomly sampling genes from raw genome assemblies.
-- **Orthology-free**: ROADIES automates the process of species tree inference from their raw genome assemblies without requiring any intermediate gene annotations or orthologous groups. It allows multi-copy gene trees (inferred from homologous regions) and does not require the challenging and error-prone step of orthologous detection prior to gene tree inference. 
-- **Alignment-free**: ROADIES does not require any input alignment to be provided, as all alignments required for gene tree inference are constructed within the ROADIES pipeline itself.
-- **Discordance-aware**: Instead of single-copy genes, ROADIES considers multi-copy genes while analyzing species tree and takes care of the possible gene discordances such as paralogs, horizonal gene transfer, incomplete lineage sorting. It uses a state-of-the-art and statistically consistent discordance-aware method to combine gene trees into a species tree.
+- **Orthology-free**: ROADIES automates the process of species tree inference from their raw genome assemblies without requiring any intermediate gene annotations or orthologous groups. It allows multi-copy gene trees (inferred from homologous regions) and does not require the challenging step of orthologous detection prior to gene tree inference. 
+- **Annotation-free**: ROADIES does not require any input genome annotations, as ROADIES randomly samples genes within the pipeline itself.
+- **Discordance-aware**: Instead of single-copy genes, ROADIES considers multi-copy genes while analyzing species trees and takes care of the possible gene discordances such as paralogs, horizontal gene transfer, incomplete lineage sorting. It uses a state-of-the-art and statistically consistent discordance-aware method to combine gene trees into a species tree.
 - **Scalability**: ROADIES handles both small-scale and large-scale datasets efficiently, including diverse life forms such as mammals, flies, and birds. ROADIES also scales efficiently with multiple cores and produces faster results.
 - **Flexibility**: ROADIES allows users to tune the tradeoff between accuracy and runtime by configuring the parameters and tailoring the pipeline to their specific needs.
 - **Debugging options**: ROADIES provides multiple plots as output for graphical analysis, making it easier for the user to debug. 
@@ -44,9 +44,9 @@ ROADIES pipeline consists of multiple stages, from raw genome assemblies to spec
 
 ROADIES supports multiple modes of operation based on various user requirements considering the tradeoff between accuracy and runtime. 
 
-- **Accurate-Mode**: This is the default mode of operation and is preferred for accuracy-critical use cases. Here, the multiple sequence alignment stage is performed by [PASTA](https://github.com/smirarab/pasta) and the tree building stage is governed by [RAxML-NG](https://github.com/amkozlov/raxml-ng).
-- **Fast-Mode**: This mode of operation is preferred for achieving faster results, for runtime-critical use cases. Here, the multiple sequence alignment and tree building stage is performed by [MashTree](https://github.com/lskatz/mashtree).
-- **Balanced-Mode**: This mode of operation is preferred where the user wants an optimal runtime vs accuracy tradeoff. Here, the multiple sequence alignment stage is performed by [PASTA](https://github.com/smirarab/pasta), and the tree building stage is performed using [FastTree](http://www.microbesonline.org/fasttree/). 
+- **Accurate-Mode**: This is the default mode of operation and is preferred for accuracy-critical use cases. Here, the multiple sequence alignment stage is performed by [PASTA](https://github.com/smirarab/pasta) and the tree-building stage is governed by [RAxML-NG](https://github.com/amkozlov/raxml-ng).
+- **Fast-Mode**: This mode of operation is preferred for achieving faster results, for runtime-critical use cases. Here, the multiple sequence alignment and tree-building stage is performed by [MashTree](https://github.com/lskatz/mashtree).
+- **Balanced-Mode**: This mode of operation is preferred where the user wants an optimal runtime vs accuracy tradeoff. Here, the multiple sequence alignment stage is performed by [PASTA](https://github.com/smirarab/pasta), and the tree-building stage is performed using [FastTree](http://www.microbesonline.org/fasttree/). 
 
 !!! Note
     These modes of operation can be modified using command line argument `--mode` (details mentioned in the [Usage](index.md#other-command-line-arguments) section).
@@ -56,7 +56,7 @@ ROADIES supports multiple modes of operation based on various user requirements
 The initial count of the genes is crucial to get the accurate species tree at the end. The number of genes sufficient for getting the accurate tree also varies with datasets. Hence, ROADIES incorporates an adaptive algorithm for establishing accurate trees by tracking its confident scores. It performs multiple iterations of the entire pipeline and stops if it gets the confident tree, otherwise it continues with more gene counts. The confidence of the tree is evaluated by the confidence of its branches (or local posterior probability). The tree having most of the confident branches with high posterior probability are considered to be confident and stable. 
 
 !!! Note
-    [ASTRAL-Pro2](https://github.com/chaoszhang/A-pro) provides the information of all the internal nodes in the form of quartets (and its support values such as local posterior probability) for every species tree per iteration. ROADIES gathers this information and keeps track of all the nodes with high support values. If the percentage change in the number of highly supported nodes gets minimal with a given number of iterations, then we say that the species tree is now converged.
+    [ASTRAL-Pro2](https://github.com/chaoszhang/A-pro) provides the information of all the internal nodes in the form of quartets (and its support values, such as local posterior probability) for every species tree per iteration. ROADIES gathers this information and keeps track of all the nodes with high support values. If the percentage change in the number of highly supported nodes gets minimal with a given number of iterations, then we say that the species tree is now converged.
 
 !!! Note
     Users have the option to run ROADIES in converge mode using `--converge` argument (details mentioned in [Usage](index.md#other-command-line-arguments) section).