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index.md

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-## Uncalled: a Utility for Nanopore Current ALgnment to Large Expanses of DNA
+# UNCALLED: a Utility for Nanopore Current ALgnment to Large Expanses of DNA
 
-### Real-time targeted sequencing
-
-Uncalled enables targeted sequencing by directly aligning raw nanopore signal to a reference and selectively ejecting reads via [adaptive sampling](https://nanoporetech.com/resource-centre/adaptive-sampling-oxford-nanopore) (AKA ReadUntil).
-
-For more information see the [main branch](https://github.com/skovaka/UNCALLED), or [read the paper](https://www.nature.com/articles/s41587-020-0731-9)
+The UNCALLED repository contains two related tools for nanopore signal alignment/mapping: UNCALLED for signal mapping and adaptive sampling, and Uncalled4 for accurate signal alignment, analysis, and visualization.
 
 ## Uncalled4: visualization and analysis of nanopore RNA and DNA signal alignments
 
-We are actively developing our next major release titled Uncalled4: a toolkit for alignment, analysis, and visualization of raw nanopore RNA and DNA signal. Uncalled4 features interactive alignment visualizations, an alignment algorithm guided by Guppy metadata, methods for comparing Tombo and Nanopolish alignments, and epigenetic modification detection statistics. This will eventually be merged into the main codebase, but in the meantime a development version can be found on the [uncalled4 branch](https://github.com/skovaka/UNCALLED/tree/uncalled4).
+We are actively developing Uncalled4: a toolkit for alignment, analysis, and visualization of raw nanopore RNA and DNA signal. Uncalled4 features interactive alignment visualizations, an alignment algorithm guided by basecaller metadata, methods for training pore k-mer models, and epigenetic modification detection statistics. This was initially developed as an extension of UNCALLED (see below), but we now plan to migrate it to a dedicated repository soon. In the meantime it is currently availible in the [uncalled4 branch](https://github.com/skovaka/UNCALLED/tree/uncalled4) of the UNCALLED repository.
 
 [![Uncalled4 logo](assets/img/logo4.png "Uncalled4 logo")](https://github.com/skovaka/UNCALLED/tree/uncalled4)
+
+### UNCALLED: real-time targeted sequencing via raw signal mapping
+
+UNCALLED enables targeted sequencing by directly aligning raw nanopore signal to a reference and selectively ejecting reads via [adaptive sampling](https://nanoporetech.com/resource-centre/adaptive-sampling-oxford-nanopore) (AKA ReadUntil). This is a distinct algorithm from Uncalled4 (above), focused on rapid seed mapping rather than accurate end-to-end alignment.
+
+For more information see the [main branch](https://github.com/skovaka/UNCALLED), or [read the paper](https://www.nature.com/articles/s41587-020-0731-9)
+