more readme changes
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-## TreeTime: maximum likelihood dating and ancestral inference for phylogenetic trees
+## TreeTime: maximum likelihood dating and ancestral sequence inference
### Overview
@@ -11,6 +11,8 @@ To optimize the likelihood of time-scaled phylogenies, TreeTime uses an iterativ
The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree.
The package is designed to be used as a stand-alone tool on the command-line or as a library used in larger phylogenetic analysis work-flows.
+In addition to scripting TreeTime or using it via the command-line, there is also a small web server at [treetime.ch](https://treetime.ch).
+
![Molecular clock phylogeny of 200 NA sequences of influenza A H3N2](https://raw.githubusercontent.com/neherlab/treetime_examples/master/figures/tree_and_clock.png)
#### Features
@@ -29,7 +31,7 @@ The package is designed to be used as a stand-alone tool on the command-line or
+ [Homoplasy analysis](#homoplasy-analysis)
+ [Mugration analysis](#mugration-analysis)
* [Example scripts](#example-scripts)
- * [Comparable/related Tools](#comparable-tools)
+ * [Related tools](#related-tools)
* [Projects using TreeTime](#projects-using-treetime)
* [Building the documentation](#building-the-documentation)
* [Developer info](#developer-info)
@@ -91,7 +93,7 @@ will reconstruct ancestral sequences at internal nodes of the input tree.
The full list if options is available by typing `treetime ancestral -h`.
A detailed explanation of `treetime ancestral` with examples is available at [treetime_examples/ancestral.md](https://github.com/neherlab/treetime_examples/blob/master/ancestral.md)
-#### Homoplasy scan
+#### Homoplasy analysis
Detecting and quantifying homoplasies or recurrent mutations is useful to check for recombination, putative adaptive sites, or contamination.
TreeTime provides a simple command to summarize homoplasies in data
```bash
@@ -121,7 +123,7 @@ The following scripts illustrate how treetime can be used to solve common proble
HTML documentation of the different classes and function is available at [here](https://treetime.biozentrum.unibas.ch/doc).
-### Comparable/related Tools
+### Related tools
There are several other tools which estimate molecular clock phylogenies.
* [Beast](http://beast.bio.ed.ac.uk/) relies on the MCMC-type sampling of trees. It is hence rather slow for large data sets. But BEAST allows the flexible inclusion of prior distributions, complex evolutionary models, and estimation of parameters.
