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_sources/change_log/index.rst.txt

@@ -8,12 +8,6 @@ Change log
 
 Major changes to PhyKIT are summarized here.
 
-**2.0.1**:
-- added arguments to exclude sites with gaps in the pairwise identities and saturation functions.
-
-**2.0.0**:
-Codebase overhaul to make PhyKIT more mem efficient and faster. For example, using list comprehension when appropriate.
-
 **1.21.0**:
 The partition file outputted from the create_concat function has been updated to the following format:
 - column 1: alignment name

_sources/usage/index.rst.txt

@@ -456,8 +456,7 @@ Genome Biology and Evolution (2017), doi: 10.1093/gbe/evx147.
 
 Options: |br|
 *<alignment>*: first argument after function name should be an alignment file |br|
-*-v/\\-\\-verbose*: optional argument to print identity per pair|br|
-*-e/--exclude_gaps*: if a site has a gap, ignore it
+*-v/\\-\\-verbose*: optional argument to print identity per pair
 
 |
 
@@ -1409,7 +1408,6 @@ Biology (2011), doi: 10.1371/journal.pbio.1000602.
 Options: |br|
 *-a/\\-\\-alignment*: an alignment file |br|
 *-t/\\-\\-tree*: a tree file |br|
-*-e/--exclude_gaps*: if a site has a gap, ignore it |br|
 *-v/\\-\\-verbose*: print out patristic distances and uncorrected |br|
 distances used to determine saturation 
 

change_log/index.html

@@ -83,10 +83,6 @@
 <span id="id1"></span><h1>Change log<a class="headerlink" href="#change-log" title="Link to this heading"></a></h1>
 <hr class="docutils" />
 <p>Major changes to PhyKIT are summarized here.</p>
-<p><strong>2.0.1</strong>:
-- added arguments to exclude sites with gaps in the pairwise identities and saturation functions.</p>
-<p><strong>2.0.0</strong>:
-Codebase overhaul to make PhyKIT more mem efficient and faster. For example, using list comprehension when appropriate.</p>
 <p><strong>1.21.0</strong>:
 The partition file outputted from the create_concat function has been updated to the following format:
 - column 1: alignment name

usage/index.html

@@ -509,8 +509,7 @@ <h3>Pairwise identity<a class="headerlink" href="#pairwise-identity" title="Link
 </div>
 <p>Options: <br/>
 <em>&lt;alignment&gt;</em>: first argument after function name should be an alignment file <br/>
-<em>-v/\-\-verbose</em>: optional argument to print identity per pair|br|
-<em>-e/–exclude_gaps</em>: if a site has a gap, ignore it</p>
+<em>-v/\-\-verbose</em>: optional argument to print identity per pair</p>
 <div class="line-block">
 <div class="line"><br /></div>
 </div>
@@ -1319,7 +1318,6 @@ <h3>Saturation<a class="headerlink" href="#saturation" title="Link to this headi
 <p>Options: <br/>
 <em>-a/\-\-alignment</em>: an alignment file <br/>
 <em>-t/\-\-tree</em>: a tree file <br/>
-<em>-e/–exclude_gaps</em>: if a site has a gap, ignore it <br/>
 <em>-v/\-\-verbose</em>: print out patristic distances and uncorrected <br/>
 distances used to determine saturation</p>
 </section>