docs(input-files): edit pass

nextstrain · Jan 8, 2024 · 2099bcf · 2099bcf
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diff --git a/docs/user/input-files/01-sequence-data.md b/docs/user/input-files/01-sequence-data.md
@@ -7,6 +7,8 @@ Nextclade Web: accepted in "Provide sequences" drag & drop box. A remote URL is
 Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format).
 
 A set of viral nucleotide sequences to be analyzed. Also referred to as [query sequences](../terminology.md#query-sequence).
+These sequences must use a DNA alphabet (`U`/Uracil is not accepted at the moment).
+However, ambiguous [IUPAC characters](https://www.bioinformatics.org/sms/iupac.html) are allowed.
 
 Note: each id must start with `>`, plain text without header is not accepted.
 

diff --git a/docs/user/input-files/03-genome-annotation.md b/docs/user/input-files/03-genome-annotation.md
@@ -2,7 +2,7 @@
 
 A tab separated table describing the genes of the virus (name, frame, position, etc.)
 
-The annotation is required for codon-aware alignment, for translation of CDS (CoDing Sequences), and for calling of aminoacid mutations. Without annotation (sometimes called genemap), peptide sequences will not be output and aminoacid mutations will not be detected. Without annotation the nucleotide alignment step will not be informed by codon information (see: [Algorithm: Sequence alignment](../algorithm/01-sequence-alignment) and [Algorithm: Translation](../algorithm/02-translation)).
+The annotation is required for codon-aware alignment, for translation of CDS (CoDing Sequences), and for calling of amino acid mutations. Without annotation (sometimes called genemap), peptide sequences will not be output and amino acid mutations will not be detected. Without annotation the nucleotide alignment step will not be informed by codon information (see: [Algorithm: Sequence alignment](../algorithm/01-sequence-alignment) and [Algorithm: Translation](../algorithm/02-translation)).
 
 Accepted formats: [GFF3](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md).
 

diff --git a/docs/user/input-files/05-pathogen-config.md b/docs/user/input-files/05-pathogen-config.md
@@ -136,11 +136,11 @@ Example:
 }
 ```
 
-#### `defaultGene`
+#### `defaultCds`
 
 Optional `str`. The default gene/CDS to be shown in Nextclade web. If not provided, the nucleotide alignment is shown. Example value: `"S"`.
 
-#### `geneOrderPreference`
+#### `cdsOrderPreference`
 
 Optional `array[str]`. Order in which genes are shown in Nextclade web dropdown. Example value ["S", "ORF1a", "N", "E"]