From eaf58ab66d0423c80f61c81505899d779a14becd Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 19 Dec 2023 15:55:08 +0100 Subject: [PATCH] edit msa doc file again --- docs/user/MSA.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/user/MSA.md b/docs/user/MSA.md index c62337f5..04ea268b 100644 --- a/docs/user/MSA.md +++ b/docs/user/MSA.md @@ -1,6 +1,6 @@ # Multiple Sequence Alignment -The commande msa compute multiple sequence alignement of any partition of the pangenome. The command uses [mafft](https://mafft.cbrc.jp/alignment/software/) with default options to perform the alignment. Using multiple cpus is recommended as multiple alignment can be quite demanding in computational resources. +The commande `msa` compute multiple sequence alignement of any partition of the pangenome. The command uses [mafft](https://mafft.cbrc.jp/alignment/software/) with default options to perform the alignment. Using multiple cpus with the `--cpu` argument is recommended as multiple alignment can be quite demanding in computational resources. This command can be used as follow: @@ -22,19 +22,19 @@ for example will compute MSA for all the persistent gene families. ppanggolin msa -p pangenome.h5 --partition persistent ``` -Supported partitions are `core`, `persistent`, `shell`, `cloud`, `softcore`, `accessory`. If you wish to have additional filters, you can raise an issue in the [issue tracker](https://github.com/labgem/PPanGGOLiN/issues) with your demand, or write a PR directly (see [here](../dev/contribute.md) for instruction on how to contribute), most possibilites should be quite straightforward to add. +Supported partitions are `core`, `persistent`, `shell`, `cloud`, `softcore`, `accessory`. If you need specific filters, you can submit a request in the [issue tracker](https://github.com/labgem/PPanGGOLiN/issues) with your requirements. You can also directly implement the new filter and submit a Pull Request (instructions for contribution can be found [here](../dev/contribute.md)). Most filters should be quite straightforward to add. -### source +### Chose to align dna or protein sequences with `--source` -You can specify whether to use dna or protein sequences for the MSA by using --source. It uses protein sequences by default. +You can specify whether to use `dna` or `protein` sequences for the MSA by using `--source`. It uses protein sequences by default. ```bash ppanggolin msa -p pangenome.h5 --source dna ``` -### phylo +### Write a single whole MSA file with `--phylo` -It is also possible to write a single whole genome MSA file, which many phylogenetic softwares accept as input, by using the --phylo option as such: +It is also possible to write a single whole genome MSA file, which many phylogenetic softwares accept as input, by using the `--phylo` option as such: ```bash ppanggolin msa -p pangenome.h5 --phylo