Output.md

@@ -20,11 +20,11 @@ Reference tree topology with node numbers matching the numbers in the [RUG*](#ru
 Table in comma-separated-values of terminals organized according to how much they affect match-split distances.
 
 #### MATCHES*
-Saves the number of the trees that matches the selected topology.
+Saves the number of trees that match the selected topology.
 
 * First column gives the tree numbers that correspond to lines in the [TREE*](#tree) file.
 * Second column gives any comments that were given between square brackets with the input trees (e.g., tree costs). If no comment was given with a tree, reports "No_Comment" instead.
-* The third columns gives the tree number in the original input file. 
+* The third column gives the tree number in the original input file. 
 
 #### RUG*
 
@@ -32,17 +32,17 @@ Sensitivity plots in SVG format. Files are named according to node numbers in th
 
 #### SA*
 
-Table using tab-separated-values.
+Table using tab-separated values.
 
-* The line numbers are in the first column and corresponds to each of the clades in the tree.
+* The line numbers are in the first column and correspond to each of the clades in the tree.
 * The second column has the number of trees that contain and do not contain (separated by ":") the clade in each of the input files (separated by ",").
 * The third column has the total number of trees that have and do not have the clade (separated by ":").
-* The forth column has the percentage of trees that have the clade.
-* The fifth column has the terminals that comprises the clade.
+* The fourth column has the percentage of trees that have the clade.
+* The fifth column has the terminals that comprise the clade.
 
 **Schematic explanation of the SA* tables:**
 
-| Line numbers | Clade prevalece per file | Total clade prevalence | Percentage | Terminals comprising the clade |
+| Line numbers | Clade prevalence per file | Total clade prevalence | Percentage | Terminals comprising the clade |
 | :----------- | :----------------------------- | :--------------------- | :--------- | :----------------------------- |
 | | absolute values (number of trees) | absolute values (number of trees) | 0-100% | Comma-separated teminal names |
 | | yes:no, yes:no ... yes:no | yes:no | | |
@@ -67,37 +67,37 @@ Distance matrix for all the trees being compared. This matrix is saved in table-
 
 #### BRACKETS*
 
-Temporary file kept only if verbose is on.
+The temporary file is kept only if verbose is on.
 
 Saves the position of open (1st column) and close (2nd column) brackets in the corresponding tree saved in the [TREE*](#tree) file.
 
 #### CLADES*
 
-Temporary file kept only if verbose is on.
+The temporary file is kept only if verbose is on.
 
 All the clades in the corresponding tree saved in the [TREE*](#tree) file.
 
 #### COMMENTS*
 
-Temporary file kept only if verbose is on.
+The temporary file is kept only if verbose is on.
 
-Saves any comments (e.g., tree costs) provided between square brackets in the input trees. Comments corresponds to the tree in the same line in the [TREE*](#tree) file.
+Saves any comments (e.g., tree costs) provided between square brackets in the input trees. Comments correspond to the tree in the same line in the [TREE*](#tree) file.
 
 #### PRUNED*
 
-Temporary file kept only if verbose is on or if the search for wildcard taxa is executed manually with arguments -m.
+The temporary file is kept only if verbose is on or if the search for wildcard taxa is executed manually with arguments -m.
 
-Pruned trees. File name corresponds to the terminal that was removed from the trees in this file.
+Pruned trees. The filename corresponds to the terminal that was removed from the trees in this file.
 
 #### MSDIST*
 
-Temporary file kept only if verbose is on.
+The temporary file is kept only if verbose is on.
 
 Results from [MSdist](http://www.kaims.pl/~dambo/msdist/index.html) analysis, including absolute distance values.
 
 #### SPLITS*
 
-Temporary file kept only if verbose is on.
+The temporary file is kept only if verbose is on.
 
 All the splits in the corresponding tree saved in the [TREE*](#tree) file.
 
@@ -105,11 +105,11 @@ All the splits in the corresponding tree saved in the [TREE*](#tree) file.
 
 ### Output files from [ybyra_apo.py](https://gitlab.com/MachadoDJ/ybyra/blob/master/ybyra_apo.py)
 
-Output files uses only the project name as prefix.
+Output files use only the project name as the prefix.
 
 #### Tree files
 
-A single strict consensus reference tree with node numbers is printed in two different formats. The *_nodes.tre file is in [NEWICK](http://evolution.genetics.washington.edu/phylip/newicktree.html) format. The other .tre file is in TREAD format. Each node has a number that corresponds to a sensitivity plot in SVG format. Branch lengths corresponds to the branch prevalence among all trees.
+A single strict consensus reference tree with node numbers is printed in two different formats. The *_nodes.tre file is in [NEWICK](http://evolution.genetics.washington.edu/phylip/newicktree.html) format. The other .tre file is in TREAD format. Each node has a number that corresponds to a sensitivity plot in SVG format. Branch lengths correspond to the branch prevalence among all trees.
 
 #### SVG files
 
@@ -118,7 +118,7 @@ YBYRÁ generates color-coded boxes to indicate if a derived state occurs only in
 Files are named according to node numbers in the output [tree files](#tree-files).
 
 * character-states are at the center of each cell
-* Character number are at the bottom of each cell (character counting starts at 0, not 1)
+* Character numbers are at the bottom of each cell (character counting starts at 0, not 1)
 * Black cells are unique, non-homoplastic synapomorphies
 * Red cells are unique, homoplastic synapomorphies
 * Blue cells are non-unique, homoplastic synapomorphies
@@ -128,6 +128,14 @@ Files are named according to node numbers in the output [tree files](#tree-files
 
 ![CategorizedSynapomorphies](uploads/8fb76c6bb79e20cf2d3e454f72bdafe9/CategorizedSynapomorphies.png)
 
+**Explanation of the color code:**
+
+- I) Ambiguous synapomorphies (white boxes): indicates an ambiguous transformation that would be ignored by `ybyra_apo_apolish.py` and therefore is never shown with a plesiomorphic to apomorphic state transformation on YBYRÁ's output files
+- II) Unambiguous synapomorphies:
+  - II.I) Unique, non-homoplastic (black boxes): indicates a transformation leading to a unique and exclusive character state that is shared among all terminals of the corresponding clade and that and not present in any other terminal
+  - II.II) Unique, homoplastic (red boxes): indicates a transformation leading to a character state shared among all members of the corresponding clade but that can be found on other terminals of different clades
+  - II.III) Non-unique, homoplastic (blue boxes): indicates a transformation leading to a character state that is not shared by all members of the corresponding clade and that may or may not arise more than once in the tree
+
 **Example of character categorization:**
 
 ![example](uploads/1a5947ec05869bd16ff736301fca97c1/example.png)
@@ -142,4 +150,4 @@ Any output text messages given by [TNT](http://www.lillo.org.ar/phylogeny/tnt/)
 
 #### CSV files
 
-Two tables in comma-separated-values are given. The *_characters.csv holds the complete categorization of characters. A summary of the non-ambiguous synapomorphies is given in the other .csv file.
+Two tables in comma-separated values are given. The *_characters.csv holds the complete categorization of characters. A summary of the non-ambiguous synapomorphies is given in the other .csv file.
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