https://github.com/evolbioinfo/pastml
Ancestral character reconstruction and visualisation for rooted phylogenetic trees
https://github.com/evolbioinfo/pastml
ancestral-character-reconstruction maximum-likelihood parsimony phylogenetics phylogeography visualisation
Last synced: 8 months ago
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Ancestral character reconstruction and visualisation for rooted phylogenetic trees
- Host: GitHub
- URL: https://github.com/evolbioinfo/pastml
- Owner: evolbioinfo
- License: gpl-3.0
- Created: 2018-11-15T13:59:04.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-02-26T16:57:04.000Z (over 2 years ago)
- Last Synced: 2024-04-29T08:20:13.049Z (about 2 years ago)
- Topics: ancestral-character-reconstruction, maximum-likelihood, parsimony, phylogenetics, phylogeography, visualisation
- Language: Python
- Homepage: https://pastml.pasteur.fr
- Size: 36.2 MB
- Stars: 25
- Watchers: 8
- Forks: 5
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PastML
__PastML__ provides fast methods for Ancestral Character Reconstruction (ACR) and visualisation
on rooted phylogenetic trees. Given a rooted tree and its node annotations, it can either visualise them as-is,
or infer ancestral node states based on the tip states, with a selection of maximum likelihood and parsimonious methods.
The result is then visualised as a zoomable html map.
[](https://doi.org/10.1093/molbev/msz131)
[](https://github.com/evolbioinfo/pastml/releases)
[](https://anaconda.org/bioconda/pastml)
[](https://pypi.org/project/pastml/)
[](https://pypi.org/project/pastml/)
[](https://hub.docker.com/r/evolbioinfo/pastml/tags)
[](tests)
#### Article
Ishikawa. SA, Zhukova. A, Iwasaki W, Gascuel O (2019) __A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios__. [_Molecular Biology and Evolution_, msz131](https://doi.org/10.1093/molbev/msz131).
## How it works
For detailed description of the ACR methods, and visualization procedure used in __PastML__ please visit our [help page](https://pastml.pasteur.fr/help).
## Try it online
Try __PastML__ at [pastml.pasteur.fr](https://pastml.pasteur.fr)
# Input data
As an input, one needs to provide a **rooted** phylogenetical tree in [newick](https://en.wikipedia.org/wiki/Newick_format) format,
and a table containing tip states,
in tab-delimited (by default) or csv format (to be specified with *--data_sep ,* option).
### Example
You can download [HIV1-A in Albania data](examples/Albania/data) as an example.
Let's assume that the tree and annotation files are in the Downloads folder,
and are named respectively Albanian.tree.152tax.tre and data.txt.
The data.txt is a comma-separated file, containing tip ids in the first column,
and Country in the second column, i.e.:
id | Country
----- | -----
98CMAJ6932 | Africa
98CMAJ6933 | Africa
96CMAJ6134 | Africa
00SEAY5240 | WestEurope
... | ...
02GRAY0303 | Greece
97YUAF9960 | EastEurope
# Installation
There are 3 alternative ways to run __pastml__ on your computer: with [docker](https://www.docker.com/community-edition), [singularity](https://www.sylabs.io/singularity/) or in python3.
## Run with docker
### Basic usage
Once [docker](https://www.docker.com/community-edition) is installed, run the following command:
```bash
docker run -v :/data:rw -t evolbioinfo/pastml --tree /data/ --data /data/ --data_sep --columns --html_compressed /data/
```
For example, to reconstruct and visualise the ancestral Country states for Albanian data,
one needs to run the following command:
```bash
docker run -v ~/Downloads:/data:rw -t evolbioinfo/pastml --tree /data/Albanian.tree.152tax.tre --data /data/data.txt --columns Country --html_compressed /data/Albanian_map.html --data_sep ,
```
This will produce a file Albanian_map.html in the Downloads folder,
that can be viewed with a browser.
#### Help
To see advanced options, run
```bash
docker run -t evolbioinfo/pastml -h
```
## Run with singularity
### Basic usage
Once [singularity](https://www.sylabs.io/guides/2.6/user-guide/quick_start.html#quick-installation-steps) is installed, run the following command:
```bash
singularity run docker://evolbioinfo/pastml --tree --data --columns --html_compressed --data_sep
```
For example, to reconstruct and visualise the ancestral Country states for Albanian data,
one needs to run the following command:
```bash
singularity run docker://evolbioinfo/pastml --tree ~/Downloads/Albanian.tree.152tax.tre --data ~/Downloads/data.txt --columns Country --html_compressed ~/Downloads/Albanian_map.html --data_sep ,
```
This will produce a file Albanian_map.html in the Downloads folder,
that can be viewed with a browser.
#### Help
To see advanced options, run
```bash
singularity run docker://evolbioinfo/pastml -h
```
## Run in python3
### Windows
For **Windows** users, we recommend installing __pastml__ via [Cygwin environment](https://www.cygwin.com/).
First instal python3 and pip3 from the Cygwin packages. Then install __pastml__:
```bash
pip3 install pastml
```
### All other platforms
You can install __pastml__ for python with or without [conda](https://conda.io/docs/), following the procedures described below:
#### Installing with conda
Once you have conda installed create an environment for __pastml__ with python3, here we name it pastmlenv:
```bash
conda create --name pastmlenv python=3
```
Then activate it:
```bash
source activate pastmlenv
```
Then install __pastml__ in it:
```bash
pip install pastml
```
#### Installing without conda
Make sure that pyhon3 and pip3 are installed, then install __pastml__:
```bash
pip3 install pastml
```
### Basic usage in a command line
If you installed __pastml__ via conda, do not forget to first activate the dedicated environment (here named pastmlenv), e.g.
```bash
source activate pastmlenv
```
To run __pastml__:
```bash
pastml --tree --data --columns --html_compressed --data_sep
```
For example, to reconstruct and visualise the ancestral Country states for Albanian data,
one needs to run the following command:
```bash
pastml --tree ~/Downloads/Albanian.tree.152tax.tre --data ~/Downloads/data.txt --columns Country --html_compressed ~/Downloads/Albanian_map.html --data_sep ,
```
This will produce a file Albanian_map.html in the Downloads folder,
that can be viewed with a browser.
#### Help
To see advanced options, run:
```bash
pastml -h
```
### Basic usage in python3
```python
from pastml.acr import pastml_pipeline
# Path to the table containing tip/node annotations, in csv or tab format
data = "~/Downloads/data.txt"
# Path to the tree in newick format
tree = "~/Downloads/Albanian.tree.152tax.tre"
# Columns present in the annotation table,
# for which we want to reconstruct ancestral states
# (for Albanian data we only have one column, but multiple columns are also allowed)
columns = ['Country']
# Path to the output compressed map visualisation
html_compressed = "~/Downloads/Albanian_map.html"
# (Optional) path to the output tree visualisation
html = "~/Downloads/Albanian_tree.html"
pastml_pipeline(data=data, data_sep=',', columns=columns, name_column='Country', tree=tree,
html_compressed=html_compressed, html=html, verbose=True)
```
### Examples
See the [examples folder](https://github.com/evolbioinfo/pastml/tree/master/examples) for ideas :)