From a21198722d428e5b243268da681905b89f1cc7ce Mon Sep 17 00:00:00 2001
From: Adam Hockenberry <hockenberry.adam@gmail.com>
Date: Tue, 19 May 2020 12:20:07 -0500
Subject: [PATCH] fixing typos in readme

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 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 13204fa..0c6965b 100644
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@@ -15,9 +15,9 @@ Pre-print available at: <https://www.biorxiv.org/content/10.1101/2020.05.13.0948
 
 ## Overview and important caveats
 
-The BACPHLIP software is designed to test whether a given phage genome (`.fasta` formatted) is likely to be either temperate (lysogenic) or virulent (lytic). The software makes this determination by searching for a particular set of what are hypothesized to be "temperate-specific" protein domains. As such, the default assumption is that any given input file is a virulent (lytic) phage. Depending on the number and identity of various proteins that are found, this default assumption may be updated to indicate that the sequence is in fact temperate. **BACPHLIP does not perform any checks on whether the input sequence is even a phage.** Thus, random stretches of DNA will be called virulent phages (assuming that no relevant domains are found within the random sequence) not because there are any idications of the sequence being a virulent phage, but rather because no data overturns the starting assumption (that you provied the program with a phage). Similarly strange results will occur if you provide BACPHLIP with whole bacterial chromosomes, these will likely be called temperate phages simply because it's likely that several of the relevant "temperate domains" will be found somewhere within the chromosome. 
+The BACPHLIP software is designed to test whether a given phage genome (`.fasta` formatted) is likely to be either temperate (lysogenic) or virulent (lytic). The software makes this determination by searching for a particular set of what are hypothesized to be "temperate-specific" protein domains. As such, the default assumption is that any given input file is a virulent (lytic) phage. Depending on the number and identity of various proteins that are found, this default assumption may be updated to indicate that the sequence is in fact temperate. **BACPHLIP does not perform any checks on whether the input sequence is even a phage.** Thus, random stretches of DNA will be called virulent phages (assuming that no relevant domains are found within the random sequence) not because there are any idications of the sequence being a virulent phage, but rather because no data overturns the starting assumption (that you provided the program with a phage). Similarly strange results will occur if you provide BACPHLIP with whole bacterial chromosomes, these will likely be called temperate phages simply because it's likely that several of the relevant "temperate domains" will be found somewhere within the chromosome. 
 
-Finally, we recommend that users read through all documentation here as well as the manuscript (referenced above). Our software was trained on a dataset consisting almost entirely of phages from the order *Caudovirales*, most of which infect hosts in teh orders *Actinobacteria*, *Gammaproteobacteria*, and *Bacilli*. We urge caution when using the software on species outside of these orders, butt his fact may change as we update and expand training set data in future releases. 
+Finally, we recommend that users read through all documentation here as well as the manuscript (referenced above). Our software was trained on a dataset consisting almost entirely of phages from the order *Caudovirales*, most of which infect hosts in the orders *Actinobacteria*, *Gammaproteobacteria*, and *Bacilli*. We urge caution when using the software on species outside of these orders, but this fact may change as we update and expand training set data in future releases. 
 
 ## Installation