====== Instructions for readers ======

Each text consists of a number of files, each of which is one version of the text. They might be transcriptions of manuscripts, of printed sources, or born-digital texts. They are encoded in TEI XML format, and the XML source can be viewed, by clicking the {{wiki:view_source.png|View pagesource}} button, or downloaded, by clicking the {{wiki::upama_export.png|Export as...}} button and selecting “TEI XML”.

==== Generating an apparatus of variants ====

In order to compare different versions of a text, you can generate an apparatus of variants:
	* First, pick one version of the text to be the base text. 
	* Then, in the sidebar, click {{wiki:other_witnesses_button.png|Other witnesses}}
	* Select one or more other witnesses that you want to compare to the base text. 
{{ wiki:other_witnesses.png }}
	* Then, click {{wiki:generate_apparatus.png|Generate apparatus}} 

=== Apparatus options ===

There are a number of additional options for how to deal with TEI tags, punctuation, and orthography. [[wiki:tei|TEI tags]] can be set to to either:
	* Hide: removes the tag and its contents completely
	* Ignore all: ignores the tag and its contents in the comparison
	* Ignore tag only: ignores the tag but keeps the text inside the tag for comparison
	* Include: considers the tag to be significant in the comparison

See [[wiki:orthography|Punctuation and Orthography]] for information on the options and algorithms used to filter out insignificant variation.

==== Using the apparatus ====

	* The variant readings will appear in the right margin. Move the cursor over a variant reading in order to see the lemma highlighted in the base text.
{{wiki:negative-apparatus.png|Negative apparatus}}
	* Click on a siglum to go to the transcription of that witness.
	* A siglum with a dotted underline indicates the presence of a minor orthographic variation. Move the cursor of the underlined siglum to display it.
	* In the text, click and drag to highlight a passage to show a positive apparatus. 
{{wiki:positive_apparatus.png|Positive apparatus}}


==== Other tools ====

	* In the positive apparatus, click the {{wiki:matrix_button.png|matrix}} button to show a variant matrix.

{{wiki:variant_matrix.png|Variant matrix}}

	* Click the {{wiki:tree_button.png|tree}} button, if available, to show a cladistic tree.

{{wiki:tree_view.png|Cladistic tree view}}

==== Export options ====

Any text, with or without an apparatus, can be exported as TEI XML, LaTeX, or FASTA.

	* In order to compile the exported LaTeX file, you will need the reledmac package. By default, the file uses the [[https://brill.com/page/1228|Brill typeface]] as well as a few characters from [[https://chchch.github.io/PedanticIndic/|Pedantic Devanagari]]. These can be swapped out for different fonts by changing the corresponding lines in the LaTeX file.

	* FASTA is a format used in bioinformatics. The exported FASTA file treats each text as a sequence of letters, with no spaces. They can be aligned using the  [[https://mafft.cbrc.jp/alignment/software/|MAFFT]] sequence alignment program in text mode. The resulting alignment can be used to produce phylogenetic trees and networks, using software such as [[https://www.mesquiteproject.org/|Mesquite]] or [[https://en.wikipedia.org/wiki/SplitsTree|SplitsTree]].