PyPI 官网下载 | pastml-1.9.28.tar.gz

# 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. #### 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 <path_to_the_folder_containing_the_tree_and_the_annotations>:/data:rw -t evolbioinfo/pastml --tree /data/<tree_file.nwk> --data /data/<annotation_file.csv> --data_sep <separator_eg_,> --columns <column1 column2 ...> --html_compressed /data/<output_map.html> ``` 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 <path/to/tree_file.nwk> --data <path/to/annotation_file.csv> --columns <column1 column2 ...> --html_compressed <path/to/output/map.html> --data_sep <separator_eg_,> ``` 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 <path/to/tree_file.nwk> --data <path/to/annotation_file.csv> --columns <column1 column2 ...> --html_compressed <path/to/output/map.html> --data_sep <separator_eg_,> ``` 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 :)