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README.md
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......@@ -163,7 +163,7 @@ Or, if you used singularity, just remove the downloaded image: `rm -r panacota.i
`PanACoTA` contains 6 different subcommands:
- `prepare` (download genomes from refseq if you want to, or give your input database, to run a filtering quality control)
- `prepare` (download genomes from refseq if you want to, or give your input database, to run a filtering quality control). To help you find NCBI species taxid you need, you can use their [taxonomy browser](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi).
- `annotate` (annotate all genomes of the dataset, after a quality control)
- `pangenome` (generate pan-genome)
- `corepers` (generate core-genome or persistent-genome)
......@@ -184,6 +184,8 @@ When using singularity, just replace `PanACoTA` by `./panacota.img`:
./panacota.img <subcommand_name> <arguments_for_subcommand>
./panacota.img -h
It also provides a subcommand `PanACoTA all` to run all modules in a row.
## <a name="example"></a> Examples
We provide a folder, `Examples`, containing genomic sequences (in `Examples/genomes`) and examples of input files (in `Examples/input_files`) for the software.
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doc/source/develop.rst
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......@@ -3,18 +3,13 @@ Work on PanACoTA code
=====================
This part is for people who want to work on developing `PanACoTA` package: adding new features, correcting bugs etc.
PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https://gitlab.pasteur.fr/aperrin/pipeline_annotation
Installing ``PanACoTA`` in development mode
===========================================
If you want to install ``PanACoTA`` while still working on modifying the scripts, type:
.. code-block:: bash
./make develop
If you want to install ``PanACoTA`` while still working on modifying the scripts, use ``./make develop`` instead of ``./make install`` once you have cloned the git repository.
Your changes will then be taken into account. As you installed the package, you will be able to run it from any directory in your computer.
......@@ -54,7 +49,7 @@ If you want to run only a specific test, run::
py.test test/test_<unit or functional>/<test_file.py>::<test_name>
When you run tests (all of them or individual ones), it will also always generate the coverage report. Open ``htmlcov/index.html`` on your browser if you want to check code coverage of your new function/module. The online version can be found `here <http://aperrin.pages.pasteur.fr/pipeline_annotation/htmlcov/>`_, and is automatically updated at each push on master branch.
When you run tests (all of them or individual ones), it will also always generate the coverage report. Open ``htmlcov/index.html`` on your browser if you want to check code coverage of your new function/module. The online version can be found `here <http://aperrin.pages.pasteur.fr/pipeline_annotation/htmlcov/>`_, and is automatically updated at each push on master branch of the gitlab repository.
.. warning:: If you add new features, or modify existing scripts please complete/update the tests!
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doc/source/index.rst
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......@@ -15,8 +15,8 @@ Amandine PERRIN, Eduardo P.C. ROCHA (2020). PanACoTA: A modular tool for massive
whatis
starting
examples
usage
examples
about
......
doc/source/starting.rst
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......@@ -6,12 +6,15 @@ Starting with PanACoTA
``PanACoTA`` is a Python package, developed in Python 3.6.
Dependencies
Installation
============
Dependencies
------------
``PanACoTA`` is written in **python3**. So, you need python3 (and pip3 for installation) to run it.
There are several external dependencies. Install only the one(s) you need, according to the module(s) you want to use:
Then, ``PanACoTA`` has several external dependencies. If you use :ref:`Singularity <singularity>` installation (for ex. to run on a cluster), you do not need to install any dependency. Otherwise, install only the one(s) you need, according to the module(s) you want to use:
- For prepare module: `mash <https://mash.readthedocs.io/en/latest/>`_ (to filter genomes)
- For annotate module: `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (to uniformly annotate your genomes)
......@@ -41,83 +44,123 @@ For FastTree, we advise to download C code from `here <http://www.microbesonline
You can then add the output ``FastTreeMP`` to your ``$PATH`` to be able to run it from everywhere.
Installation:
=============
Downloading and updating
Installation and update:
------------------------
You have different possibilities to install ``PanACoTa``.
.. warning:: If you plan to work on the scripts, choose the development installation (see :doc:`Developer documentation <develop>`).
From pip
********
|pip|
You can get ``PanACoTA`` source code by downloading an archive of a given release (zip, tar.gz), or by cloning its github repository. By cloning the github repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
.. |pip| image:: https://badge.fury.io/py/PanACoTA.svg
:target: https://badge.fury.io/py/PanACoTA
A very simple way to install the last stable version. This will install files in your python site-packages folder.
.. code-block:: bash
pip install panacota
And to get new version
.. code-block:: bash
pip install panacota --upgrade
If you have permission issues, you can either use 'sudo' before the previous command lines to install it as root, or add the ``--user`` option to install it locally.
From Github repository
**********************
.. _clone:
This allows you to get the very last version, and be able to test the last enhancements before they are uploaded to the other platforms (pip, conda, singularity...). For that, go to where you want to install it ``(<your_dir>)``, and type:
.. code-block:: bash
git clone https://github.com/gem-pasteur/PanACoTA.git
ve your github login, and password.
This will create a repository called ``PanACoTA``. Go inside this repository (``cd PanACoTA``) to install the software, as described hereafter.
This will create a repository called ``PanACoTA``, containing the content of this Github repository. To install PanACoTA, and be able to launch it from anywhere:
.. code-block:: bash
cd PanACoTA
./make
If a new version of ``PanACoTA`` is released, and you want to use it, type the following command to update the source code:
If you have permission issues, you can either use 'sudo' before the previous command lines to install it as root, or add the ``--user`` option to install it locally.
To upload to new version, go back to your repository:
.. code-block:: bash
cd <your_dir>/PanACoTA
git pull
./make upgrade
Then, you will be able to upgrade to the new version (see :ref:`Upgrade section <upgrade>`).
From singularity image
**********************
.. _singularity:
.. _installing:
|singularity|
Installing ``PanACoTA``
--------------------------
.. |singularity| image:: https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg
:target: https://singularity-hub.org/collections/4724
To install ``PanACoTA``, from its directory, type:
Very useful if you do not have permission rights on the computer, such as, for example, on a cluster. The other advantage is that you do not need to install any dependence (except singularity itself of course). Singularity image includes all of them. You just have to download 1 file, and nothing will be installed anywhere on your computer.
First, download the singularity image:
.. code-block:: bash
./make
singularity pull --name panacota.img shub://gem-pasteur/PanACoTA[:<version>]
If you want a specific version, like version 1.0, specify ``shub://gem-pasteur/PanACoTA:1.0``.
or
To get latest version:
.. code-block:: bash
./make install
singularity pull --name panacota.img shub://gem-pasteur/PanACoTA
You will then be able to use the package from any directory in your computer,
just as any other software.
(This is the same as ``singularity pull --name panacota.img shub://gem-pasteur/PanACoTA:latest``)
.. note:: If you have permission issues, you can either use ``sudo`` before the previous command lines to install it as root, or, if you do not have root access (or prefer a local installation), use ``./make --user`` to install it locally.
It will replace your file ``panacota.img`` by a new one corresponding to the latest version.
.. warning:: If you plan to work on the scripts, choose the development installation (see :doc:`Developer documentation <develop>`).
.. _uninstall:
From zip version
****************
Uninstalling ``PanACoTA``
----------------------------
For people wanting to download source code of a specific version, we provide releases. You can download last one here:
If you don't want ``PanACoTA`` anymore, uninstall it by typing:
|zip|
.. code-block:: bash
.. |zip| image:: https://img.shields.io/github/release/gem-pasteur/PanACoTA.svg
:target: https://github.com/gem-pasteur/PanACoTA/releases
./make uninstall
.. note:: If you have permission issues, and installed the package as root, use ``sudo`` before the previous command line to uninstall it.
.. _installing:
.. _upgrade:
Uninstalling ``PanACoTA``
-------------------------
Upgrade to new version
----------------------
.. _uninstall:
If you want to install a new version of ``PanACoTA``:
If you don't want ``PanACoTA`` anymore uninstall it by typing:
.. code-block:: bash
git pull # update source code to the new version
./make upgrade # upgrade to the new version
.. note:: If you have permission issues, and installed the package as root, use ``sudo`` before the second command line (``sudo ./make upgrade``) to upgrade. Or, if you installed the package locally, use ``./make upgrade --user`` to upgrade this local version.
pip uninstall panacota # If you installed from pip
./make uninstall # If you installed from github repository
If you installed it by downloading a zip file, :ref:`Uninstall it <uninstall>`, and install the new version (by cloning gitlab repository, or downloading the new zip file).
Or, if you used singularity, just remove the downloaded image: ``rm -r panacota.img``.
Quick run
......@@ -125,7 +168,7 @@ Quick run
``PanACoTA`` contains 6 different subcommands:
- ``prepare`` (download genomes from refseq if you want to, or give your input database, to run a filtering quality control)
- ``prepare`` (download assemblies from refseq if you want to, or give your input database, to run a filtering quality control). To help you find NCBI species taxid you need, you can use their `taxonomy browser <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi>`_
- ``annotate`` (annotate all genomes of the dataset, after a quality control)
- ``pangenome`` (generate pan-genome)
- ``corepers`` (generate core-genome or persistent-genome)
......@@ -144,20 +187,11 @@ Each subcommand has its own options and inputs. To get the list of required argu
PanACoTA <subcommand> -h
Running with singularity image
==============================
We provide a singularity image, to help running PanACoTA on a cluster.
First, download the singularity image::
singularity pull --name panacota.img shub://gem-pasteur/PanACoTA[:version]
If you want a specific version, like version 1.0, specify ``shub://gem-pasteur/PanACoTA:1.0``. If you want the latest version, use ``shub://gem-pasteur/PanACoTA`` or ``shub://gem-pasteur/PanACoTA:latest``.
Then, you can run PanACoTA in the same way as previously, using:
When using singularity, just replace ``PanACoTA`` by ``./panacota.img``:
.. code-block:: bash
./panacota.img -h # to get help on the whole PanACoTA program
./panacota.img <subcommand_name> <arguments_for_subcommand> # to run a module of PanACoTA on your data.
./panacota.img <subcommand_name> <arguments_for_subcommand>
./panacota.img -h
It also provides a subcommand ``PanACoTA all`` to run all modules in a row.
doc/source/usage.rst
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......@@ -4,14 +4,16 @@ Running PanACoTA - help by module
``PanACoTA`` contains 6 subcommands, for the different steps:
- ``prepare`` (download genomes from refseq if you want to, or give your input database, to run a filtering quality control)
- ``prepare`` (download genomes from refseq if you want to, or give your input database, to run a filtering quality control). To help you find NCBI species taxid you need, you can use their `taxonomy browser <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi>`_
- ``annotate`` (annotate all genomes of the dataset, after a quality control)
- ``pangenome`` (generate pan-genome)
- ``corepers`` (generate core-genome or persistent-genome)
- ``align`` (align core/persistent families)
- ``tree`` (infer phylogenetic tree from persistent genome)
You can run them by typing::
We also provide a subommand ``all`` to run all modules in a row.
You can run each subcommand by typing::
PanACoTA <subcommand_name> <arguments_for_subcommand>
......@@ -19,32 +21,34 @@ Each subcommand has its own options and inputs. To get the list of required argu
PanACoTA <subcommand> -h
General information
===================
Here are the options shared by all subcommands:
.. note:: In the example command lines, we put ``<>`` around the fields that you have to replace by the information corresponding to what you want.
- ``-h`` or ``--help``: show help on subcommand, as described here above.
- ``--quiet``: do not write anything in stdout nor stderr. Log files are still created, so you can check what is running.
- ``-v`` or ``--verbose``: be more verbose:
+ ``-v`` will add warnings in stderr (by default, only errors are displayed in stderr, warnings are just in log files),
+ ``-vv`` will do the same as ``-v``, and also add details to stdout (by default, only info is written to stdout)
.. note:: In the example command lines, we put ``<>`` around the fields that you have to replace by the information corresponding to what you want.
For example, if we write ``command -D <seqfile>`` and the sequence file you want to use is in your current directory and is called ``my_sequence.fa``, then you should write ``command -D my_sequence.fa``.
.. note:: In the example command lines, commands between ``[]`` are optional, meaning that you can run the command line without this part.
.. note:: In the example command lines, commands between ``[]`` are optional, meaning that you can run the command line without this part.
Example: your sequence file is the same as previously, and the default parameters are ``-t=10`` and ``-i=0.5``. Therefore, if we write ``command -D <seqfile> [-t <num> -i <percentage>]``. You can run either:
- ``command -D my_sequence`` (using default parameters for both options: 10 and 0.5)
- ``command -D my_sequence -t 8`` (specifying ``t=8`` option and default ``i=0.5``)
- ``command -D my_sequence`` (using default parameters for both options: 10 and 0.5)
- ``command -D my_sequence -t 8`` (specifying ``t=8`` option and default ``i=0.5``)
- ``command -D my_sequence -i 0.9`` (default ``t=10`` and specified ``i=0.9``)
- ``command -D my_sequence -t 8 -i 0.9`` (specifying both options: ``t=8`` and ``i=0.9``)
according to your needs (if default values are ok, you do not need to specify the option).
Here are the options shared by all subcommands:
- ``-h`` or ``--help``: show help on subcommand, as described here above.
- ``--quiet``: do not write anything on stdout nor stderr. Log files are still created, so you can check what is running.
- ``-v`` or ``--verbose``: be more verbose:
+ ``-v`` will add warnings in stderr (by default, only errors are displayed in stderr, warnings are just in log files),
+ ``-vv`` will do the same as ``-v``, and also add details to stdout (by default, only info is written to stdout)
We will now describe each subcommand, with its options.
......@@ -57,8 +61,8 @@ You can see all required arguments and available options with::
The ``prepare`` module works in 3 steps:
1) Downloading sequences from refseq
2) Quality control to filter genomes in terms of sequence quality
1) Downloading assemblies from refseq
2) Quality control to filter assemblies in terms of sequence quality
3) Filtering step dedicated to remove redundant and miss-classified genomes, based on Mash genetic distance.
You can choose to skip steps 1 and 2. Here, we describe how to run this module, starting from step 1, skipping step 1 (starting from step 2), and skipping steps 1 and 2 (starting from step 3).
......@@ -66,9 +70,9 @@ You can choose to skip steps 1 and 2. Here, we describe how to run this module,
Inputs
------
Your input will depend on the step from which you are starting.
Your input will depend on the step from which you are starting.
- If your start from the beginning, your input is a NCBI taxid and/or a NCBI species.
- If your start from the beginning, your input is a NCBI taxid and/or a NCBI species. You can also specify which assembly level(s) you want to download
- If you start from step 2, your input will be a database of fasta sequences, in :ref:`sequences format <seq>`.
- If you start from step 3, your input will be the database as previously, as well as the LSTINFO output of :ref:`step 2 <step2>`.
......@@ -78,17 +82,20 @@ Outputs
Genome sequences
^^^^^^^^^^^^^^^^
All sequences are in fasta format, as described in :ref:`sequences format <seq>`.
In your output directory, you will find:
- Only if you started from step 1: A folder called ``refseq/bacteria``, containing 1 folder per genome (called with the genome accession number), and, inside, the genome sequence in fasta.gz format, and the MD5SUMS of this file.
- Only if you started from step 1: A folder called ``Database_init``, containing all genomes downloaded in fasta format
- Only if you started from step 1: A folder called ``refseq/bacteria``, containing 1 folder per assembly (called with the assembly accession number), and, inside, the assembly sequence in fasta.gz format, and the MD5SUMS of this file.
- Only if you started from step 1: A folder called ``Database_init``, containing all assemblies downloaded from refseq in fasta format
- Only if you started from step 1 or 2: A folder called ``tmp_files`` containing your genomic sequences, split at each stretch of at least 5 ``N`` (see :ref:`sequences format <seq>` for more details on the splitting part).
Discarded files
^^^^^^^^^^^^^^^
``discarded-by-L90_nbcont-<datasetname>.lst``
This file contains the list of genomes discarded by the quality control step:
......@@ -104,8 +111,8 @@ Example:
.. code-block:: text
orig_name to_annotate gsize nb_conts L90
<outdir>/Database_init/genome1.fst <outdir>/<tmp>/genome1.fst_prepare-split5N.fna 9808 2 2
<outdir>/Database_init/genome3-chromo.fst-all.fna <outdir>/<tmp>/genome3-chromo.fst-all.fna_prepare-split5N.fna 8817 3 3
<outdir>/Database_init/genome1.fst <outdir>/<tmp>/genome1.fst_prepare-split5N.fna 9808 2 2
<outdir>/Database_init/genome3-chromo.fst-all.fna <outdir>/<tmp>/genome3-chromo.fst-all.fna_prepare-split5N.fna 8817 3 3
<outdir>/Database_init/genome2.fst <outdir>/<tmp>/genome2.fst_prepare-split5N.fna 10711 4 4
<outdir>/Database_init/genome4.fst <outdir>/<tmp>/genome4.fst_prepare-split5N.fna 7134 1 1
......@@ -114,9 +121,9 @@ Example:
This file contains the list of genomes discarded by the filtering step:
1. path to the genome original sequence
2. path to the genome which discarded genome 1.
3. distance between genome 1. and genome 2. (which is not inside the given thresholds)
- path to the genome original sequence
- path to the genome which discarded genome 1.
- distance between genome 1. and genome 2. (which is not inside the given thresholds)
Example:
......@@ -156,23 +163,37 @@ Running from step 1
To download genomes, and then process them by the `prepare` filters, run::
PanACoTA prepare [-t <NCBI taxid> -s <NCBI species]
PanACoTA prepare [-t <NCBI species taxid> -s <NCBI species> -l <assembly_level(s)>]
Give at least one of ``-t`` or ``-s`` parameters. With:
- ``-t <NCBI taxid>``: the taxid provided by the NCBI for the species you want to study.
- ``-s <NCBI species>``: the name of the species, as written by the NCBI. Give name between quotes.
If you do not want to download all assemblies in refseq, but only genomes with specific assembly levels, use option ``-l <level(s)>``. Give it a comma separated list of assembly levels you want to download, between 'all', 'complete', 'chromosome', 'scaffold', 'contig' (default is 'all').
For example, if we want to download refseq assemblies of *Acetobacter orleanensis*. With the `taxonomy browser <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=104099&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock>`_, we can find its corresponding NCBI species taxid: "104099".
To download all assembly levels::
PanACoTA prepare -t 104099 -s "Acetobacter orleanensis"
Or, to download only complete and scaffold assemblies::
PanACoTA prepare -s "Acetobacter orleanensis" -l complete,scafflod
Give at least one of those 2 parameters. With:
Only one of 'species taxid' and 'species name' argument is enough.
- ``-t <NCBI taxid>``: the taxid provided by the NCBI for the species you want to study. For example, taxid for *E. coli* is 562 (see `NCBI taxonomy browser <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=562>`_)
- ``-s <NCBI species>``: the name of the species, as written by the NCBI. Give name between quotes (for example "escherichia coli")
Running from step 2
-------------------
If you already have your genomes, run::
If you already have your assemblies and/or genomes, run::
PanACoTA prepare --norefseq -o <outdir> [-d <db_dir>]
With:
- ``<outdir>``: the directory where you want to save your results (no need to create the directory before, the program will do it).
- ``<outdir>``: the directory where you want to save your results (no need to create the directory before, the program will do it).
- ``<db_dir>``: directory where your database sequences are. By default, it will search to `<outdir>/Database_init`. So, if your sequences are already there, you do not need to add this option.
......@@ -553,21 +574,21 @@ All other information than the genome names in the first columns will be ignored
protein files
^^^^^^^^^^^^^
Each genome in your list_file corresponds to a protein file in ``dbdir``. This protein file is in multi-fasta format,
and the headers must follow this format:
``<genome-name_without_space_nor_dot>_<numeric_chars>``.
For example ``my-genome-1_00056`` or ``my_genome_1_00056`` are valid protein headers.
Each genome in your list_file corresponds to a protein file in ``dbdir``. This protein file is in multi-fasta format,
and the headers must follow this format:
``<genome-name_without_space_nor_dot>_<numeric_chars>``.
For example ``my-genome-1_00056`` or ``my_genome_1_00056`` are valid protein headers.
.. warning:: All proteins of a genome must have the same ``<genome-name_without_space_nor_dot>``. Otherwise, they won't be considered in the same genome, which will produce errors in your core or persistent genome!
Ideally, you should follow the 'gembase_format', ``<name>.<date>.<strain_num>.<contig><place>_<num>``
(as it is described in :ref:`LSTINFO folder format <lstf>`, field "name of the sequence annotated"),
Ideally, you should follow the 'gembase_format', ``<name>.<date>.<strain_num>.<contig><place>_<num>``
(as it is described in :ref:`LSTINFO folder format <lstf>`, field "name of the sequence annotated"),
where the genome name, shared by all proteins of the genome.
If your protein files were generated by ``PanACoTA annotate``, they are already in this format!
Those fields will be used to sort genes inside pangenome families. They are sorted by species ``<genome-name_without_space_nor_dot>``
(if you do a pangenome containing different species),
Those fields will be used to sort genes inside pangenome families. They are sorted by species ``<genome-name_without_space_nor_dot>``
(if you do a pangenome containing different species),
strain number ``<strain_num>`` (inside a same species), and protein number ``<num>`` (inside a same strain). If you do not use gembase format,
families will only be sorted by protein number (the ``<numeric_chars>`` part).
......@@ -596,14 +617,14 @@ This fictive pangenome contains 4 families. Family 1 contains 4 proteins, family
Qualitative matrix
^^^^^^^^^^^^^^^^^^
You will also find a qualitative matrix corresponding to your pangenome.
Its columns correspond to the different families, and its lines to the different genomes.
In each cell, there is a 1 if the genome has a member in the family, or 0 if not.
You will also find a qualitative matrix corresponding to your pangenome.
Its columns correspond to the different families, and its lines to the different genomes.
In each cell, there is a 1 if the genome has a member in the family, or 0 if not.
For example, the qualitative matrix corresponding to the pangenome example just above is:
.. code-block:: text
fam_num 1 2 3 4
fam_num 1 2 3 4
ESCO.0217.00001 1 1 0 0
ESCO.0217.00002 1 0 0 0
ESCO.1216.00003 1 0 0 0
......@@ -618,13 +639,13 @@ This file can be used as an input to do GWAS analysis with `treeWAS <https://git
Quantitative matrix
^^^^^^^^^^^^^^^^^^^
You will also find a quantitative matrix. As for the qualitative matrix, columns correspond to the different families,
and lines to the different genomes. But here, each cell contains the number of members from the given genome in the given family.
You will also find a quantitative matrix. As for the qualitative matrix, columns correspond to the different families,
and lines to the different genomes. But here, each cell contains the number of members from the given genome in the given family.
Here is the quantitative matrix corresponding to the pangenome example above:
.. code-block:: text
fam_num 1 2 3 4
fam_num 1 2 3 4
ESCO.0217.00001 1 1 0 0
ESCO.0217.00002 2 0 0 0
ESCO.1216.00003 1 0 0 0
......@@ -676,8 +697,8 @@ with:
- ``-i <min_id>``: minimum percentage of identity required to put 2 proteins in the same family. When doing a pangenome at the species level, we commonly use a threshold of 80% of identity.
This will create (if not already existing) your ``outdir``, and, after execution, this directory will contain your pangenome file,
as well as other useful files. If you did not specify a pangenome filename (``-f`` option), the default pangenome name will be
This will create (if not already existing) your ``outdir``, and, after execution, this directory will contain your pangenome file,
as well as other useful files. If you did not specify a pangenome filename (``-f`` option), the default pangenome name will be
``Pangenome-<dataset_name>.All.prt-clust-<min_id>-mode<mode_num_given>_<current_date_and_time>.tsv.lst``:
- ``<pangenome_file or default>``: your pangenome file, which format is described :ref:`here above<panfile>`
......@@ -956,7 +977,7 @@ Corresponding to this phylogenetic tree:
Do tree
-------
By default, 'tree' subcommand will use `IQtree <http://www.iqtree.org/>`_ software to infer the phylogenetic tree.
By default, 'tree' subcommand will use `IQtree <http://www.iqtree.org/>`_ software to infer the phylogenetic tree.
To infer the tree from your alignment file, run:
.. code-block:: bash
......
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