minor grammar fix for RAxML

rknx · rknx · commit 0bc7c1761f5b · 2022-10-20T23:35:26.000-04:00
diff --git a/_optionals/60-bootstrapped_trees.md b/_optionals/60-bootstrapped_trees.md
@@ -12,12 +12,12 @@ such as the stability of tree topology.
 One way to show this is using bootstrap values, 
 which is the probability that a particular node
 (i.e. a dichotomous branching with a particular set of samples in each branch)
-appearing among a large number of trees generated 
+appears among a large number of trees generated 
 while resampling within the sequence alignment.
 Bootstrap values are often used in the same fashion as confidence intervals.
 
 A common method for creating bootstrapped trees using RAxML consists of 
-3 step approach:
+a 3 step approach:
 - Generate a few maximum likelihood (ML) trees.
 - Generate many bootstrapped trees.
 - Apply the bootstrap information to the best ML tree.
@@ -26,7 +26,7 @@ A common method for creating bootstrapped trees using RAxML consists of
 
 Maximum likelihood tree generation is computationally expensive, 
 but the resulting tree is considered superior to other rapid methods.
-Thus, we'll generate a small number of ML trees.
+Thus, we' usually generate a small number of ML trees (16 in the following example).
 
 ~~~
 $ raxmlHPC -T 8 -m GTRGAMMA -p 144 -# 16 -s input.fasta -n treeML -w outdir
diff --git a/_site/01-unix/index.html b/_site/01-unix/index.html
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diff --git a/_site/02-slurm/index.html b/_site/02-slurm/index.html
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diff --git a/_site/03-blast/index.html b/_site/03-blast/index.html
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diff --git a/_site/04-parse/index.html b/_site/04-parse/index.html
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diff --git a/_site/05-tree/index.html b/_site/05-tree/index.html
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diff --git a/_site/10-more_unix/index.html b/_site/10-more_unix/index.html
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diff --git a/_site/20-text_process/index.html b/_site/20-text_process/index.html
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diff --git a/_site/30-extra_tools/index.html b/_site/30-extra_tools/index.html
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diff --git a/_site/40-awesome_bioinfo/index.html b/_site/40-awesome_bioinfo/index.html
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diff --git a/_site/50-multiple_gene_copies/index.html b/_site/50-multiple_gene_copies/index.html
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diff --git a/_site/60-bootstrapped_trees/index.html b/_site/60-bootstrapped_trees/index.html
@@ -19,7 +19,7 @@
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-    <meta http-equiv="last-modified" content="2022-10-20 16:21:04 -0400">
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@@ -316,12 +316,12 @@ <h2>Overview</h2>
 One way to show this is using bootstrap values, 
 which is the probability that a particular node
 (i.e. a dichotomous branching with a particular set of samples in each branch)
-appearing among a large number of trees generated 
+appears among a large number of trees generated 
 while resampling within the sequence alignment.
 Bootstrap values are often used in the same fashion as confidence intervals.</p>
 
 <p>A common method for creating bootstrapped trees using RAxML consists of 
-3 step approach:</p>
+a 3 step approach:</p>
 <ul>
   <li>Generate a few maximum likelihood (ML) trees.</li>
   <li>Generate many bootstrapped trees.</li>
@@ -332,7 +332,7 @@ <h3 id="generating-an-ml-tree">Generating an ML tree</h3>
 
 <p>Maximum likelihood tree generation is computationally expensive, 
 but the resulting tree is considered superior to other rapid methods.
-Thus, we’ll generate a small number of ML trees.</p>
+Thus, we’ usually generate a small number of ML trees (16 in the following example).</p>
 
 <div class="language-bash highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="gp">$ </span>raxmlHPC <span class="nt">-T</span> 8 <span class="nt">-m</span> GTRGAMMA <span class="nt">-p</span> 144 -# 16 <span class="nt">-s</span> input.fasta <span class="nt">-n</span> treeML <span class="nt">-w</span> outdir
 
diff --git a/_site/CODE_OF_CONDUCT.html b/_site/CODE_OF_CONDUCT.html
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