diff --git a/README.md b/README.md
index a46dfa2..d46f23b 100644
--- a/README.md
+++ b/README.md
@@ -13,12 +13,18 @@
 |
 |
+
+ | Python bindings: |
+  |
+  |
+ |
+
## Features
-* Align two genomic sequences while allowing for template switches.
-* Visualise the alignment with template switch jumps.
+* Align two genomic sequences while allowing for template switch mutations (TSMs).
+* Visualise the alignment with template switching jumps.
## Installation
@@ -33,6 +39,14 @@
If you ever want to update to a new release, simply run `cargo install tsalign` again.
+### Python bindings
+
+1. Install the Python package manager [`pip`](https://pypi.org/project/pip/).
+
+2. Run `pip install tsalign`.
+
+3. Refer to [the Python bindings README](python_bindings/README.md) for more information.
+
### From Source (For Developers)
1. Install the rust toolchain by going to [rustup.rs](https://rustup.rs/) and following the instructions.
@@ -91,7 +105,7 @@ This does not pertain the special `|` character if `--use-embedded-rq-ranges` is
If you want to compute an alignment without template switches, you can use the `--no-ts` parameter.
This can be useful for comparing the optimal template switching alignment with the optimal alignment without template switches.
-### Visualisation
+### SVG/PNG Visualisation
To visualise the alignment, you can use the `tsalign show` subcommand.
For an optimal experience, compute both the alignment with template switches and the alignment without template switches.
@@ -102,28 +116,27 @@ tsalign align -p pair.fa -o alignment.toml -c sample_tsa_config --memory-limit 1
tsalign align -p pair.fa -o alignment-no-ts.toml -c sample_tsa_config --memory-limit 1000000000 --no-ts
```
-Then, create the visualisation as follows (`-t` is for plain text):
+Then, create the visualisation in SVG format as follows:
```bash
-tsalign show -i alignment.toml -n alignment-no-ts.toml -t
+tsalign show -i alignment.toml -n alignment-no-ts.toml -s alignment.svg
```
-
-Note that `-t` supports only simple cases of template switches, and may crash for more complicated cases.
-For a more detailed and robust visualisation, use the parameter `-s visualisation.svg` to render the visualisation as SVG.
Since SVGs are not always well supported, you can also use the switch `-p` to render the visualisation also as PNG.
Note that the `-p` switch requires setting the `-s` parameter.
```bash
-tsalign show -i alignment.toml -n alignment-no-ts.toml -ps visualisation.svg
+tsalign show -i alignment.toml -n alignment-no-ts.toml -p -s visualisation.svg
```
-There are some switches to add more detail to the SVG and PNG visualisation.
+There are additional switches and parameters to influence the visualisation.
* `-a` adds arrows for the jumps of the alignments
* `-c` renders more of the complements of the input sequences
+* `-e` renders the heuristically computed uncertainties of a TSM with grey characters
+* `-z X` renders only `X` bases of context around the TSMs
```bash
-tsalign show -i alignment.toml -n alignment-no-ts.toml -ps visualisation.svg -ac
+tsalign show -i alignment.toml -n alignment-no-ts.toml -ps visualisation.svg -ace -z 5
```
### Setting the alignment range
@@ -156,5 +169,10 @@ ACACA|CCCAAC|GCGGG
ACAAA|CGTGTC|GCGCG
```
-Now we can run `tsalign align -p input.delimited.fa --use-embedded-rq-ranges`.
+Now we can run tsalign as follows:
+
+```bash
+tsalign align -p input.delimited.fa --use-embedded-rq-ranges
+```
+
Now, tsalign will use much less resources, as it can ignore the non-matches before and after the focus region.